LMU BioDB 2017 - User contributions [en]

User talk:Cazinge

2017-12-10T02:38:01Z

Dondi: Week 11 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:05, 16 November 2017 (PST)''

== Week 11 Feedback ==

* These "good habit" items were not met in this submission:
** Punctuality: last edit at 12:08am 11/14.
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
* Design or development term notes
** The reference for ''plug-in'' is a tertiary-source Wikipedia article.
** The PostgreSQL link is a 404.
* Article outline notes
** Outline was 1 page long in print preview.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:38, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are mostly fulfilled except:
** Acknowledgments/signature and references were added 3-7 days late.
** The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook is in brief narrative form but does convey the process of arriving at the API calls.
* GRNsight testing is complete with clear feedback on the results.
* The provided '''bash''' script specifies the instructions for arriving at the gene data, including the portions that get substituted based on the desired gene and the final URL that yields the gene data from the assigned source.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:12, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that the electronic notebook is somewhat short on detail (though the brevity is explained with a candidness that is noted). The reference list is thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on your interest primarily being on the computer science side is noted, and that’s fine as long as you continue to retain proficiency in the biology aspect even if the interest level is not that high. When developing software for others, it is important that we acquire a firsthand sense of our user base’s needs, interests, and perspective; this is how we are able to create software to truly fulfill that user base’s needs, as opposed to just checking off requirements without fully appreciating why those requirements are the way they are.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted 8 minutes late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:53, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal landed 19 minutes late…
** …in a single edit! So kind of a double-whammy there. Had you edited more granularly, some edits might have landed on time. At least that single edit had a message.
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

* Most questions and “good habit” points are fulfilled except:
** There is no link from your shared journal back to your user page.
** There is no wiki signature on your shared entry…which is somewhat ironic because you set up the template with a very clear placeholder for the signature 🤔

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment and could still use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, but was the “shmoogle” image made by you? Or did you download it? Note how a thorough notebook (or acknowledgments) would answer this question before it even gets asked.
* Your list of links was quite thorough, including the '''cgi''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted there were other IDs on this page beyond those kinds.
* The note that you did this alone causes some concern. Was this your choice? Beyond your control? If the latter, please notify Dr. Dahlquist or myself in case it needs our inquiry or intervention. Fortunately, this assignment leaned toward the computer science side, toward which you are already comfortable. In other circumstances, not having a partner would have had more negative consequences.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but your template was added late. You also made one small edit past the deadline on your shared journal entry. You were also missing the link from your User page to the [[Week 2]] assignment. Please add these links to your template if you have not done so already.
* You wrote something in the summary field for 4 of 8 saves (50%) in the period of review; since you had only received the feedback about frequency after you submitted this assignment, I am expecting that this number will be improving in subsequent weeks.
** As we discussed in class, you obviously cannot go back to fix this; we will be looking for improvement as the semester goes on. Missing a summary field here and there because you clicked "Save" too fast, is not a big deal. We aim to approach 100%, but anything above 90% is in the acceptable range.
* However, the number of total saves to your Week 2 journal entry is quite small (5). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* We do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. I can go over splicing with you and the alpha helix/beta sheet structures of proteins. I have some 3D models in my office that may be helpful.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses. '''Completed!'''
** Please make an explicit statement about your career interests and goals. '''Completed!'''
** You wrote something in the summary field for 7 of 11 saves, or 64%. We would like to see this approach 100%. '''Will do!'''
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement). '''Completed!'''
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using <nowiki>[[File:filename | visible label]]</nowiki>, please use <nowiki>[[Media:filename | visible label]]</nowiki>. '''Completed!'''
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead of “User Page”. Please make this change. '''Completed!'''
** You did not create or invoke a template on your page. Please see the instructions on the [[Week 1 ]] assignment and let us know if you have questions on how to implement this. '''Completed!'''
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:33, 12 September 2017 (PDT)’’

:: I've updated the page and added all requested features. [[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 09:43, 16 September 2017 (PDT)

User talk:Ebachour

2017-12-10T02:32:40Z

Dondi: Week 11 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:11, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:11, 16 November 2017 (PST)''

== Week 11 Feedback ==

* A number of "good habit" items were not met in this submission:
** No journal category entry.
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** Only three edits were made for the entire submission—given the amount of content on the page, this indicates insufficient granularity.
** The references section cites [[Week 14]], not [[Week 11]].
* Design or development term notes
** No definitions were provide for 9 out of the 10 terms listed. The journal entry says “Definitions covered below in outline,” but only Xcode is defined in that way; none of the other terms are.
** No citations/references are given for any of the terms (including Xcode).
* Article outline notes
** Outline was 1.3 pages long in print preview.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:32, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are mostly fulfilled except:
** The journal entry category is missing.
** The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook is in narrative form with moderate detail, conveying the process of arriving at the API calls.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
** A generic '''query''' parameter is used for filtering by taxon ID and gene name—although this generally seems to work, particularly when coupled with the '''sort=score''' parameter, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that ''specifically'' asks for a particular taxonID and a particular gene name.
** The derivation of the ID relies on ''screen-scraping''—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:17, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your journal page is missing its category and your references were somewhat minimal, but with incorrect titles! Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on being pushed more into biology than desired is noted, but this level of exposure to the biology side of things is precisely why the class is interdisciplinary. Thus, there ''are'' assignments that require biology to finish. You’ll be amazed at where this deeper learning can lead.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:12, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:56, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Your individual journal was done in a single edit! At least that single edit had a message.
** The journal category is still missing. Template template template so you don’t have to worry about this anymore!
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your acknowledgments and references were as requested except that the headings are swapped, and no signature is supplied with the acknowledgments.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap. I know that you know this, but just pointing out that when answering questions of this nature, don't make any assumptions about what the reader already knows. State as reasonably complete an answer as you can think of. Stating that you used a standard library but not naming it is sort of a gap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would become more like virtual machines than just document viewers.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 10 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I added the feedback on [[Week 2]] :) Nonetheless, here it is:
* While the bulk of your assignment was on time, your signature, Reference section, and template were added after the deadline.
** Your category was completely missing; remember to add it to your template, if you have not already done so.
* You wrote something in the summary field for 5 of 7 saves (71%) in the period of review; remember we are aiming for 100%
* The number of total saves on your individual wiki page was 7, which is a little less than would would have been expected for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except that you converted all t's to u's, which would make it an RNA sequence. Be careful to answer what was asked, which, in this case, was a DNA sequence.
* Your +2 frame had an O instead of a P in one place (a typo?).
* The +1 and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you provided the correct link to the [[Week 2]] Assignment, but forgot to change the label, which still says "Week 1".
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:08, 24 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** Your journal entry page does not have a category—just put this in your template so you don’t forget.
** There are 7 listed edits to your journal page, with comments on 5 of them. Do treat these like commits: fine-grained, always with a message.
* You supplied an electronic notebook with this assignment, but it could use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? For example, you said that the '''sed''' part “took a lot of process of elimination”—what did you try? What did you eliminate? The dead ends are useful to other readers too.
* Your hack-a-page work certainly fulfilled the instructions; the upside-down text is clever. You mentioned ''upsidedowntext.com'' in your notebook, and this should be in the acknowledgments too.
* Your list of links (2 items) was shorter than I would have hoped, given how many there were (and their variety).
* Your list of IDs was more comprehensive, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* As stated, ''upsidedowntext.com'' deserves a mention in your acknowledgments.
* As your shared journal entry and chosen quote indicate, one can certainly spend lots of time “poking around” through algorithms, whether they are what you need or not. Hope the journey itself remains rewarding, as opposed to being a plain time-suck.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed the majority of your assignment on time, but we note that you did make some changes after the deadline.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include a snail mail address on your User Page. You do not have to use your residence address, if it is off-campus. Using the “1 LMU Drive…” general campus address will be sufficient.
** Please make an explicit statement about your career interests and goals.
** As you noted in the summary field for your commit, we did not want you to do the entire assignment in one go. Generally it is a good idea to map out the outline of a page with the headers, then click on the “edit” button next to the header to work on a section individually. Somewhere in the range of 10-20 saves would have been good for this size page.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please organize your page using three levels of headers, ==, ===, and ====; you only had one level, ==, on your page.
** Your numbered list was added after the deadline. One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. You interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** Your “comment out” had incorrect syntax, so it appeared on the page. You need to use <nowiki><!--</nowiki> to open a comment, just like in HTML.
** The animated gif that you chose to upload to your page is fun, but is very distracting for someone to look at who wants to actually read your page. Would you please replace it with a static image?
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using an external link format, please use <nowiki>[[Media:filename | visible label]]</nowiki>.
** The category “Journal Entry” is missing from your page, please include it on your template.
** You acknowledged the sources you used in your Acknowledgments section, but you also need to include the statement “While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.” and include your wiki signature. This will be required every week.
** For the shared journal assignment, you forgot to sign your entry with your wiki signature. This will be a requirement each week as well.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 12 September 2017 (PDT)''

User talk:Bhamilton18

2017-12-10T02:25:11Z

Dondi: Week 11 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:00, 16 November 2017 (PST)''

== Week 11 Feedback ==

* "Good habit" item notes:
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** The wiki signature is missing from the acknowledgments section.
* Design or development term notes
** Good assortment of terms and technologies there—they are defined and cited as specified in the instructions.
* Article outline notes
** Your outline fulfills the specifications in the instructions—well done!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:25, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are almost fulfilled and on-time. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the last URL that delivers the full data for a single gene. After performing the needed '''esearch''' API calls, you want to make a final '''esummary''' API call in order to get the full dataset for the specific gene whose ID you were able to extract via '''esearch'''.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:39, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the acknowledgments were missing your wiki signature, and the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook is very thorough and detailed.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Unfortunately, the project will be the furthest we will get in the realm of web pages and database integration; hope the biology pace continues to work for you, and we’ll let the other computer science class take care of your interest in those areas.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:22, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:07, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that both your individual and shared journal entries were submitted on time.
* Your electronic lab notebook is excellent, with a good amount of detail. However, it seems like your list-formatting got messed up in places. Make sure that after you save the page, you review it to see whether it displays properly.
* Your frequency of edits is excellent and you wrote something in the summary field 100% of the time--keep up the good work.
* I also want to note that Bootstrap is considered a standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:48, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for 19 out of the 20 listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Note how both issues would be addressed by having them in a template—consider doing that.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment.
* Your hack-a-page work certainly fulfilled the instructions, and really, one can’t go wrong with pugs!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Feeling that “I’m not a natural” can certainly be a challenge, but as you stated, you enjoy puzzles at heart and in many respects computer science in general and programming in particular does share a lot with puzzles. (so do mathematical proofs—I took MATH 248 with Dr. Larson, and she kept referring to the proofs we had to do as “little puzzles”) Keeping hold of that puzzle sensibility can help with “jamming” things into your brain, and of course arriving at a solution to the puzzle certainly helps!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:36, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 23 of 34 saves (68%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 12, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, and +3 translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment, just the answers again. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to write a narrative about your process and keep your electronic lab notebook on the same page as your journal entry.
* One small note about your References section: you need to skip two lines in wiki syntax to get something to appear on a newline.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:41, 23 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You wrote something in the summary field for 18 of 37 saves, or 49%. We would like to see this approach 100%. '''Will Improve'''
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.'''Completed'''
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====. '''Completed'''
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. On the Shared Journal page, you interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.'''Completed'''
** You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in <nowiki>[[Media:filename | visible label]]</nowiki>. It will look neater if you include the label.'''Completed'''
** You included multiple categories on your page; we would prefer to see just the category “Journal Entry” instead of the ones you chose. The value of a category is that everyone is using the same ones to create the Table of Contents page.'''Completed'''
** Another idiosyncrasy of MediaWiki is that if you want something to appear on a new line, you actually have to skip two lines instead of one. If you only skip one, the content on the second line will merge with the previous line. '''Completed'''
* Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:36, 12 September 2017 (PDT)''

User talk:ArashLari

2017-12-10T02:14:29Z

Dondi: /* Week 11 Feedback */ Fix name capitalization.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 11 Feedback ==

* A number of "good habit" items were not met in this submission:
** No journal category entry.
** Nominal electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** Only one of the 6 edits has a summary.
** In the references section, the Flake entry is formatted inconsistently from the others.
* Design or development term notes
** The Kissmetrics citation is missing its corresponding entry in the references section.
* Article outline notes
** Outline was 1 page long in print preview.
** No explicit statement on the overall importance of significance of the article's content could be found. There are some notes on the importance/significant of particular items, but not of the work as a whole.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:04, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time but have the following issues:
** The journal entry category is missing.
** The references section is missing.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:18, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the journal page category is missing and there is no wiki signature in the acknowledgments section.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on biology is noted; there is definitely a lot to learn on that side. On the other hand, this degree of depth is what makes for a proper interdisciplinary class. Another perspective is that the biology majors probably feel the same way about the computer science aspect.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted ''4 days'' late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Most “good habit” items are addressed and it was submitted on time.
** The journal page is still missing a category—''add it to your template''.
** There are four (4) listed edits on your individual journal page—marginally sufficient for this week. But there were no summaries entered? You really need to treat these edits like code commits.
* Your electronic notebook has moderate detail—sufficient for the scale of this week’s journal. The narrative style works, makes your process easy to follow.
* Your Acknowledgments and References are OK, except that your wiki signature should be after just your Acknowledgments, not at the very bottom after your References.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
* However, in your answers to the questions, you used manual numbering. Don’t forget the <code>#</code> notation for numbered lists!

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, supplying comments for all 4 of the listed journal edits. The misses are:
** Four edits for an assignment of this size is still quite monolithic; find ways to work more gradually, thus saving more frequently. Build up an internal clock that makes you save your work more often.
** Your journal entry page does not have a category.—note how this would be addressed by adding it to your template—consider doing that.
** Your acknowledgments section is missing the statement that you did all of the work on your own (as specified in [[Week 1]]) as well as your wiki signature.
** Your wiki signature is also missing from your shared journal entry.
* You supplied an electronic notebook with this assignment; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Remember that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…Borat for president!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''name=code''' or '''name=output''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Regarding your chosen shared journal quote, I’d say that sometimes even a month seems slow, and something new comes up every ''day''. That’s why it’s really important to keep up and keep doing things—that’s how you can stay on top of the field.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:20, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your assignment was substantially late. Please let us know if there are any issues we can help you with in terms of assisting you with submitting your work on time.
* You wrote something in the summary field for 0 of 3 saves (0%) in the period of review; this is not counting work that was submitted late.
* You made 9 saves to your Week 2 journal entry, which is barely in the range that would be expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement and your wiki signature (see the [[Week 1]] assignment). This will be required each week.
* You are also completely missing a References section. This section is also required each week and should, at a minimum, have a correctly formatted citation to that week's assignment (APA format).
* As of the the Week 2 deadline, you were also missing most of the required links:
** User to Assignment
** User to journal entry
** Category
** Link from User page to shared journal
** The signature on your shared journal entry.
*** Make sure that your template is up-to-date with the required links and that you are invoking it on your pages, if you have not already done so.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field). Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:58, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* Your user page is missing a snail mail address.
* I don’t see an email from you regarding worries/concerns or additional information.
* Your user page was written out in a single save—not a good habit. Treat wiki pages like code: type them a little at a time, saving often and with a summary.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). All of your wiki links unnecessarily use the external full URL style, and no genuinely external link was noted in your user page.
* No bulleted list was seen in your submission.
* A numbered list was seen (in your shared journal response), but the numbers were written out manually. Use the <code>#</code> symbol to signify a numbered list item.

None of these other items were found in your submission:
* Commented-out content
* Uploaded and linked image
* Uploaded and downloadable file
* Category
* Template
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Link to user page from shared response
* Wiki signature

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:30, 11 September 2017 (PDT)

User talk:Nicolekalcic

2017-12-10T02:14:12Z

Dondi: Week 11 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:53, 16 November 2017 (PST)''

== Week 11 Feedback ==

* "Good habit" item notes:
** The electronic laboratory notebook is fairly brief and only covers the design/development term section.
* Design or development term notes
** All ten terms are defined with cited sources as specified by the instructions. Some good concepts and technologies there!
* Article outline notes
** Outline was 1 page long in print preview.
** No explicit statement on the overall importance of significance of the article's content could be found. There are some notes on the importance/significant of particular items, but not of the work as a whole.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:14, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and almost fulfilled. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified. There is, however, a slight typo in the explanation where ''Homo sapiens'' and ''Saccharomyces cerevisiae'' are referred to as genes instead of species.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:15, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your references were somewhat minimal—you definitely used more sources in this assignment than just the instructions page. Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. It’s good to hear that you are appreciating both the interdisciplinary and the collaborative aspects of the course. It can be challenging, but I think the rewards are commensurate to that challenge.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:17, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:08, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, with the exception of getting all of your work in before the due date; it’s close (last edit at 12:06am) but unfortunately the wiki tells all…
* Your lab notebook is in an easy-to-understand chronological format with good detail for what's there; however, it's a little too focused on just how you and your homework partner coordinated your work—ideally, it also includes details on how you approached the assignment work itself, including what you individually did and how you went about putting the requested content together.
* Your acknowledgments and references were as requested except that the database citations were links alone; all items in a formal references section should use a full citation style.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled except for the aforementioned due date, with edits coming in up to 12:27am.
** Note that the standard library you used here does have a name: Bootstrap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would have as much functionality as they do today.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:32, 10 October 2017 (PDT)

== Week 3 Feedback ==

You certainly were off to a good start, setting up your individual journal page with the right “good habit/best practice” instructions for all individual journal entries. However, you either ran out of time or were quite stuck. Please come to one of our office hours so that we can discuss and try to act upon any difficulties that you might be encountering.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:59, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 20 of 51 saves (39%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks.
* You made 20 saves to your Week 2 journal entry, which is at the high end of the range expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* Actually, the genetic code was cracked closer to 50 years ago--that article is a little dated. The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:36, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases course you are taking right now as your list of upper division courses (since it is the only one). You could include your other upper divisions if you want since you are neither a biology or computer science major.
** We did not receive an e-mail from you regarding your worries/concerns or if there was anything else you wanted us to know. Please send us both an e-mail, even if your answer to both questions is “no”.
** You wrote something in the summary field for 13 of 18 saves, or 72%. We would like to see this approach 100%.
** We would like you to stay away from using “----“ to create sections on your page, and simply use the header system of ==, ===, ====. The plain line should be used sparingly, for special use cases.
** Please use either numbered or bulleted lists when you need to make a list. For example, you used “-“ in your Education section. When you use * or #, MediaWiki will use proper indents and align the lines for you. I did not see an actual numbered list on your page.
** You created your template, and invoked it on your page. However, it seems like you have not added your Week 2 links to the template, but to your user page itself. You should add that information to your template, so that any page where your template is invoked will automatically be updated with that content. The category “Journal Entry” should be added to your template instead for the same reason.
* Including your artwork on the page is great! However, this is a situation where you may want to consider protecting your intellectual property. All content on this wiki is considered to be considered to be released under the Creative Commons Attribution-NonCommercial-ShareAlike license, which means that someone else can redistribute it without your permission, as long as it is attributed to you. You may or may not want this. We can discuss the implications further if you wish.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:40, 12 September 2017 (PDT)''

User talk:ArashLari

2017-12-10T02:04:29Z

Dondi: Week 11 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 11 Feedback ==

* A number of "good habit" items were not met in this submission:
** No journal category entry.
** Nominal electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** Only one of the 6 edits has a summary.
** In the references section, the Flake entry is formatted inconsistently from the others.
* Design or development term notes
** The KISSmetrics citation is missing its corresponding entry in the references section.
* Article outline notes
** Outline was 1 page long in print preview.
** No explicit statement on the overall importance of significance of the article's content could be found. There are some notes on the importance/significant of particular items, but not of the work as a whole.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:04, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time but have the following issues:
** The journal entry category is missing.
** The references section is missing.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:18, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the journal page category is missing and there is no wiki signature in the acknowledgments section.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on biology is noted; there is definitely a lot to learn on that side. On the other hand, this degree of depth is what makes for a proper interdisciplinary class. Another perspective is that the biology majors probably feel the same way about the computer science aspect.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted ''4 days'' late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Most “good habit” items are addressed and it was submitted on time.
** The journal page is still missing a category—''add it to your template''.
** There are four (4) listed edits on your individual journal page—marginally sufficient for this week. But there were no summaries entered? You really need to treat these edits like code commits.
* Your electronic notebook has moderate detail—sufficient for the scale of this week’s journal. The narrative style works, makes your process easy to follow.
* Your Acknowledgments and References are OK, except that your wiki signature should be after just your Acknowledgments, not at the very bottom after your References.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
* However, in your answers to the questions, you used manual numbering. Don’t forget the <code>#</code> notation for numbered lists!

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, supplying comments for all 4 of the listed journal edits. The misses are:
** Four edits for an assignment of this size is still quite monolithic; find ways to work more gradually, thus saving more frequently. Build up an internal clock that makes you save your work more often.
** Your journal entry page does not have a category.—note how this would be addressed by adding it to your template—consider doing that.
** Your acknowledgments section is missing the statement that you did all of the work on your own (as specified in [[Week 1]]) as well as your wiki signature.
** Your wiki signature is also missing from your shared journal entry.
* You supplied an electronic notebook with this assignment; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Remember that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…Borat for president!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''name=code''' or '''name=output''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Regarding your chosen shared journal quote, I’d say that sometimes even a month seems slow, and something new comes up every ''day''. That’s why it’s really important to keep up and keep doing things—that’s how you can stay on top of the field.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:20, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your assignment was substantially late. Please let us know if there are any issues we can help you with in terms of assisting you with submitting your work on time.
* You wrote something in the summary field for 0 of 3 saves (0%) in the period of review; this is not counting work that was submitted late.
* You made 9 saves to your Week 2 journal entry, which is barely in the range that would be expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement and your wiki signature (see the [[Week 1]] assignment). This will be required each week.
* You are also completely missing a References section. This section is also required each week and should, at a minimum, have a correctly formatted citation to that week's assignment (APA format).
* As of the the Week 2 deadline, you were also missing most of the required links:
** User to Assignment
** User to journal entry
** Category
** Link from User page to shared journal
** The signature on your shared journal entry.
*** Make sure that your template is up-to-date with the required links and that you are invoking it on your pages, if you have not already done so.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field). Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:58, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* Your user page is missing a snail mail address.
* I don’t see an email from you regarding worries/concerns or additional information.
* Your user page was written out in a single save—not a good habit. Treat wiki pages like code: type them a little at a time, saving often and with a summary.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). All of your wiki links unnecessarily use the external full URL style, and no genuinely external link was noted in your user page.
* No bulleted list was seen in your submission.
* A numbered list was seen (in your shared journal response), but the numbers were written out manually. Use the <code>#</code> symbol to signify a numbered list item.

None of these other items were found in your submission:
* Commented-out content
* Uploaded and linked image
* Uploaded and downloadable file
* Category
* Template
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Link to user page from shared response
* Wiki signature

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:30, 11 September 2017 (PDT)

User talk:Johnllopez616

2017-12-10T01:49:39Z

Dondi: Week 11 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:21, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 11 Feedback ==

* "Good habit" item notes:
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
* Design or development term notes
** Your list of design or development terms fulfills the specifications in the instructions—those are some good choices.
* Article outline notes
** Your outline fulfills the specifications in the instructions—good work!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:49, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Well done!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:12, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows excellent detail, effectively presented as bullets.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your observation that the biology content appears to be a challenge across the board is an interesting one. I hope the computer science gets equivalently challenging somehow too!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:10, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are mostly fulfilled, but this time I must really emphasize that the “this week’s journal” format of your user page template is truly showing its disadvantages now that grading has slowed down. “This week’s journal” is already at Week 7, but we needed to grade Week 5. With this time differential, the inconvenience of not having access to the class journals prior to the current week really came to the fore.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten nearly all of the “good habit” tasks down, with 15 listed edits and summary entries for all of them!
** Your inter-page links are still strictly in the “this week” version—as mentioned before, this is not bad to have, but ''also'' have the comprehensive links so that we can jump across weeks very easily.
** The journal entry links on your User page are duplicated up to Week 3.
* Your lab notebook has very good detail, with your headings and links giving it some good organization.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here! Note also your “this week” shared link—ideally, we can access all shared weeks from your user page instead of just the current one.
* Indeed the flip side of the Internet’s current indispensability and importance is now the increased impact of misinformation, hacking, and lost privacy.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** At the time that I reviewed your user page, your assignment links were restricted to “This Week’s Assignment”—not a bad idea in and of itself, but in the long run it will be more useful to have the full list available. I can see now that you have tried to add it, but at this writing you now have redundant versions, one in your template and another directly in the user page. Try to clean things up. You can keep the “This Week’s Assignment” portion, but make sure to also add the comprehensive list (as you have now started to do).
** There are 7 listed edits to your journal page, with comments on all of them. Do treat these like commits: fine-grained, always with a message. For an assignment of this size, I think additional saves would have been appropriate.
* You supplied an electronic notebook with this assignment, with your notes being well-integrated with your answers. Keep this up! You provide some good details in the spirit of openness and reproducibility, the values that we are after here. Always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, and you never know, we have a high-powered enough animation department that Rick & Morty may well visit someday!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. In addition…
* …you also realized that the values after '''seqdna''' in those links do indeed serve as IDs. You also treated URLS themselves as identifiers (and indeed they are sometimes called URIs as well), which is appropriate here.
* Your '''curl'''/'''sed''' command is largely on the money except there is a slight typo in the '''grep''' portion: You only want a leading space before <code>Frame</code>, but not <code>PRE</code>.
* Your references section is generally right, except that it is formatted like code because there is a leading space before each asterisk. Was that intentional? Either way, I think the references will look better without the leading space.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:36, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 5 of 5 saves (100%) in the period of review.
* However, the number of total saves is quite small. We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* Please indicate the ends of your protein sequence with "N-ter" and "C-ter", which is what we use to mark the ends of proteins.
* Your User page was missing the link to the [[Week 2]] assignment. Please add those links to your template and invoke your template on both your User page and individual journal entry pages for the future.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:44, 20 September 2017 (PDT)''

== Week 1 Feedback ==

I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly. We won’t count email misspellings against you 😁

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:36, 11 September 2017 (PDT)

User talk:Zvanysse

2017-12-10T01:40:02Z

Dondi: Week 11 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:01, 16 November 2017 (PST)''

== Week 11 Feedback ==

* "Good habit" item notes:
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** The references section is not formatted as specified in the [[Week 1]] instructions.
* Design or development term notes
** The agile software definition’s citation is incorrect; it lists the author’s first name rather than his last name.
* Article outline notes
** Your outline fulfills the specifications in the instructions—good work!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:40, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and almost fulfilled:
** The references section is missing.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all on-time, and mostly fulfilled (the link to the shared journal from your user page has a typo in the link). Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the acknowledgments signature is somewhat misplaced (appearing at the bottom of the page instead of right below) and the references list is quite minimal—certainly you accessed more sources than just the instructions? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
* Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
* I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Thanks for your candor regarding the difficulty level of the biology readings. Not being a biologist, I do occasionally struggle with parts too, and judging by the other shared journal entries it sounds like other classmates have similar challenges. One of our aspirations for the class is to keep everything real and to expose you to genuine current research, and a consequence of that choice is that we get exposed to readings that assume a lot more background that the class has. The good news is that this does seep in somehow, and you will emerge from the class with a lot more new knowledge than it may seem right now.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:54, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
** You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
** You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
** The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
** Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
** The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your [[Week 7]] version.
* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic lab notebook was very brief. While I enjoyed reading more about your gene and why you chose it, the intention behind the notebook is to record the details of your process. You could have included more data about your gene and detail of how you constructed your page, including syntax.
* Be sure to use the APA format for your References section.
* You made a total of 14 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* What is meant by a "standard library" is that a collection of code is available for you to re-use and adapt. In this case, Bootstrap was the standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:11, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Your user page does not have a link to the shared journal.
*** Note how the above issues would be addressed by having them in a template—consider doing that.
** Your acknowledgments section is missing the wiki signature after the statement that the journal entry is your own work.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment, and don’t hesitate to supply details as needed.
* Your hack-a-page work certainly fulfilled the instructions, and thank you for the quick ego boost of seeing my name all over the place ''':)'''
* You certainly identified some links correctly, though all but the last ('''cgi-bin/translate'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin/translate''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your chosen shared journal quote (and the sentiment you express after) is very much in line with one of my favorite computer science quotes, from Don Knuth I think, which states that programming languages aren’t intended to tell computers what to do, but to tell other programmers what you want the computer to do. This indeed goes into the core notion that programming languages are about communication between people.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:43, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* The only link to your User page was found in your wiki signature. The category was also missing. Please add these links to your template and be sure to invoke it subesquent journal entries, if you haven't already.
* You wrote something in the summary field for 0 of 10 saves (0%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks!
* The number of total saves to your Week 2 journal entry is was 8, which is a little lower than what we would expect for this exercise.
* Your translations were correct, except for leaving out one "A" from frame -1 and misreading "W" as "stop" twice. (Intersting side note, in some organisms one of the stop codons ''is'' translated as "W", just not in this exercise.)
* Your determination of which frames contained ORFs was correct.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** The conversion of T to U occurs during ''transcription''. The decoding of the genetic code occurs duing ''translation.''
* Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement (see the [[Week 1]] assignment). This will be required each week.
* In the references section, please make sure you are providing a complete citation in APA format, not just a like to the resource you used.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:19, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 15 edits were made to your user page—a good, gradual pace—but only around 7 of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Three levels of headings were requested, but only two were noted in your submission.
* The Acknowledgments section did not have a wiki signature.
* No References section was seen (recall that, at a minimum, it should have had a link to the [[Week 1]] instructions).

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:55, 11 September 2017 (PDT)

User talk:Simonwro120

2017-12-10T01:39:49Z

Dondi: Week 11 feedback.

==Comments==
Hello everyone, please feel free to leave any comments here! [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 14:17, 4 September 2017 (PDT)
----

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although your individual journal page link appears to be missing from the team template (bottom of page). For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:12, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 11 Feedback ==

* A number of "good habit" items were not met in this submission:
** Punctuality: last edit at 1:31pm 11/14.
** No link from journal entry to user page.
** No journal category entry.
** No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
** Acknowledgments section is missing signature.
* Design or development term notes
** “API” was one of the chosen terms—but you must have already known this term because we have had multiple assignments dealing with web service APIs in class. The instructions asked for terms “whose definitions you did not know when you first read the article.”
** There is no formal APA citation for the ''build server'' definition—only a link is given.
* Article outline notes
** Outline was 1 page long in print preview.
** No information was found on how the article might inform your work on the final project.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:39, 9 December 2017 (PST)

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the '''data/Gene''' web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose <code>primaryIdentifier</code> property looks like an SGD ID (that is, <code>S#########</code>).

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook is detailed and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comments on being a novice are noted—remember that everyone is a novice at everything at some point in their lives, so as long as you keep learning (you call it “re-learning” but that implies that you’ve forgotten what you’ve learned before; I think what you really mean is that you’re feeling like you’ve started over, which is true because you’ve changed majors but you’re learning ''new'' things, not things that you’ve already learned before but have now forgotten).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:27, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:06, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic notebook for this week was a little brief. If you look at your partner's notebook, she included some extra details about the syntax you used. Both of you could have said a little more about your gene in your notebook.
* You made a total of 13 edits to the wiki in the window of review and wrote something in the summary field every time, except for once (oops!)--keep up the good work.
* Don't forget to add your wiki signature to your Acknowledgments statement.
* I want to note that Bootstrap itself is a standard library--you seemed to imply in your shared journal entry that you didn't use it at all and coded your page from scratch, is that the case?

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:21, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Most of your journal was turned in on time—thank you! You did add to your reference list after the due date, at 1:11pm on September 20. Do a re-read/review of your work prior to putting it away, multiple times if needed, to make sure you catch these sooner rather than later.
* You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 17 of the listed journal edits. The misses are:
** Your acknowledgments section is missing the statement that the journal entry is your own work.
** The wiki signature that is supposed to follow that statement got pushed out to after the references section.
* You supplied an electronic notebook with this assignment, organized into headings and bullets—both good ideas. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—for example, what '''curl''' commands did you try out? What search keywords did you use and which search was the most successful? This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—that is one catty-looking dragon ''':)'''
* Your list of links is of decent size and variety, all referencing different types of supporting resources for the page.
* Of your IDs, the first two are known as element IDs and indeed fit the description of identifiers given in class and in the readings. However, '''pre_text''' and '''POST''' do not fit as well, particularly with respect to [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* Your '''curl'''/'''sed''' command is right on, and you make good use of the options available to you, especially '''output=Verbose''' to spell out some key amino acid names.
* Your chosen shared journal quote is one of the more striking ones in the article, and you might recall that when I described a model of a computer during the Week 3 class sessions, I did state that a computer’s activity was indeed centered on a clock. The “clock with benefits” phrase is a cleverer way to capture what goes on, admittedly, rather than my “fetch-decode-execute” cycle (though I think the latter is more descriptive, if drier!).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:26, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 9 of 11 saves (82%) in the period of review. This is very good, but remember, we are aiming for 100%
* The number of total saves on your individual wiki page was 10, which is just within the range of what would be expected for this assignment.
* The only link to your User page from your journal entry was in your wiki signature, and the template/category was added late. The link from your User page to the shared class journal page was also late. In the future, be sure that all the requested links are in your template and invoke them on your pages on time.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see any electronic lab notebook in your journal entry. For this assignment, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as your individual journal entry.
* One small note about your References section: you need to provide a label for the link to the Week 2 assignment.
* Also, for your Acknowledgments section, this exact statement is required each week" "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source" followed by your wiki signature.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:56, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting most of your work on time, though one edit was noticed at 3:42pm on September 5. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 32 edits were made to your user page—a good, gradual pace—but around 7 of those were missing a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* A template was successfully created, but it does not appear to be used anywhere in your submission.

For your shared journal response, no link was seen from your user page to the shared journal page. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:00, 11 September 2017 (PDT)

Main Page

2017-11-24T17:28:39Z

Dondi: /* Announcements */ Announce week 9 availability.

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL/CMSI 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Fall 2017</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

* Week 9 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 09:28, 24 November 2017 (PST)
* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 1'''
** '''Model Physiology Class:''' Monday, November 20, 10:20 AM, LSB 116.
** '''Research Seminar:''' Tuesday, November 21, 11:30 AM, LSB Auditorium.
** '''Lunch with Students:''' Tuesday, November 22, 12:30-1:30, LSB 2nd Floor Terrace.
* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page Project Links }}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Tuesdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support

=== Part 1: Building Blocks (Genetic Code and Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* Nirenberg (2004) ''Deciphering the Genetic Code''
* Kaji & Kaji (2004) ''Setting the Record Straight''
* Moody (2004) ''Digital Code of Life'', Ch. 1
* Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
** This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford (2015) ''What is Code?'']
* Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further

[http://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]
* [http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]
* [http://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]

[http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

Campbell & Heyer Chapter 4 (on [http://brightspace.lmu.edu on Brightspace])

DeRisi et al. (1997) [http://www.sciencemag.org/content/278/5338/680.full ''Science'' 278: 680-686.]

| Introduction to DNA microarray data
* Experimental design
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| rowspan="2" | [[Week 12]]

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| '''''No Week 13 assignment'''''

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| style="background: #fee; border: none" |
| style="background: #fee; border: none" | '''Final project presentations 2:00-4:00 PM'''
| style="background: #fee; border: none" |
|-
!
| Friday<br/>12/15/2017 4:30 PM
|
| '''Project deliverables due 4:30 PM'''
|
|}

== Course Information ==

=== Instructors ===

==== [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]] ====
: http://myweb.lmu.edu/kdahlqui
: '''Phone:''' (310) 338-7697
: '''E-mail:''' kdahlquist at lmu dot edu
: '''Office:''' Life Sciences Building 289
: '''Office Hours:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''Phone:''' (310) 338-5782
: '''E-mail:''' dondi at lmu dot edu
: '''Office:''' Doolan 106
: '''Office Hours:''' {{Dondi Office Hours}}

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in the Seaver College of Science and Engineering. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with web, database, or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 2:40–3:55pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is September 1. The withdrawal or credit/no-credit status deadline is November 3.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/wellness/lmucares/aboutlmucares/livethelionscode/ Lion’s code], you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# You are expected to bring the required materials to each class session.
# Cell phones and other ancillary devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by [http://studentaffairs.lmu.edu/media/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.pdf LMU Community Standards publication]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2017/. You will need to have a user account on this wiki to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email address. Messages sent to the instructors at night or on the weekend will be answered the next school day. Please cc: both instructors on all email messages related to this class.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on this wiki or [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Account for this wiki
* [http://www.github.com GitHub account]

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-to-day science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections
* Upper Division Information Literacy Flag
* Upper Division Oral Communication Flag

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at [http://brightspace.lmu.edu Brightspace].

Your work in this course will be assessed in five areas:

{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments, individual (10 points each)
| style="text-align: right" | 140
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (3 points each)
| style="text-align: right" | 42
| points
|-
| Oral presentations
| style="text-align: right" | 105
| points 
|-
| Information literacy (additional points added to two journal assignments)
| style="text-align: right" | 24
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''486'''
| '''points'''
|}

==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow.” For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every 12:01am on Tuesday Pacific time; consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries on your user talk pages.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====



In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal, specifically [https://peerj.com/computer-science/ PeerJ Computer Science]. Specific instructions will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Extra Credit ====

Students may accumulate up to 12.5 points toward their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 2.5 points with up to 5 seminars (12.5 points) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

=== Work Load Expectations ===

In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

=== University Policy on Academic Honesty ===

Loyola Marymount University is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== Americans with Disabilities Act—Special Accommodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2017/.

User talk:Zvanysse

2017-11-24T03:23:21Z

Dondi: Add week 9 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:01, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and almost fulfilled:
** The references section is missing.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all on-time, and mostly fulfilled (the link to the shared journal from your user page has a typo in the link). Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the acknowledgments signature is somewhat misplaced (appearing at the bottom of the page instead of right below) and the references list is quite minimal—certainly you accessed more sources than just the instructions? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
* Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
* I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Thanks for your candor regarding the difficulty level of the biology readings. Not being a biologist, I do occasionally struggle with parts too, and judging by the other shared journal entries it sounds like other classmates have similar challenges. One of our aspirations for the class is to keep everything real and to expose you to genuine current research, and a consequence of that choice is that we get exposed to readings that assume a lot more background that the class has. The good news is that this does seep in somehow, and you will emerge from the class with a lot more new knowledge than it may seem right now.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:54, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
** You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
** You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
** The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
** Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
** The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your [[Week 7]] version.
* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic lab notebook was very brief. While I enjoyed reading more about your gene and why you chose it, the intention behind the notebook is to record the details of your process. You could have included more data about your gene and detail of how you constructed your page, including syntax.
* Be sure to use the APA format for your References section.
* You made a total of 14 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* What is meant by a "standard library" is that a collection of code is available for you to re-use and adapt. In this case, Bootstrap was the standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:11, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Your user page does not have a link to the shared journal.
*** Note how the above issues would be addressed by having them in a template—consider doing that.
** Your acknowledgments section is missing the wiki signature after the statement that the journal entry is your own work.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment, and don’t hesitate to supply details as needed.
* Your hack-a-page work certainly fulfilled the instructions, and thank you for the quick ego boost of seeing my name all over the place ''':)'''
* You certainly identified some links correctly, though all but the last ('''cgi-bin/translate'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin/translate''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your chosen shared journal quote (and the sentiment you express after) is very much in line with one of my favorite computer science quotes, from Don Knuth I think, which states that programming languages aren’t intended to tell computers what to do, but to tell other programmers what you want the computer to do. This indeed goes into the core notion that programming languages are about communication between people.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:43, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* The only link to your User page was found in your wiki signature. The category was also missing. Please add these links to your template and be sure to invoke it subesquent journal entries, if you haven't already.
* You wrote something in the summary field for 0 of 10 saves (0%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks!
* The number of total saves to your Week 2 journal entry is was 8, which is a little lower than what we would expect for this exercise.
* Your translations were correct, except for leaving out one "A" from frame -1 and misreading "W" as "stop" twice. (Intersting side note, in some organisms one of the stop codons ''is'' translated as "W", just not in this exercise.)
* Your determination of which frames contained ORFs was correct.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** The conversion of T to U occurs during ''transcription''. The decoding of the genetic code occurs duing ''translation.''
* Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement (see the [[Week 1]] assignment). This will be required each week.
* In the references section, please make sure you are providing a complete citation in APA format, not just a like to the resource you used.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:19, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 15 edits were made to your user page—a good, gradual pace—but only around 7 of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Three levels of headings were requested, but only two were noted in your submission.
* The Acknowledgments section did not have a wiki signature.
* No References section was seen (recall that, at a minimum, it should have had a link to the [[Week 1]] instructions).

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:55, 11 September 2017 (PDT)

User talk:Aporras1

2017-11-24T03:21:11Z

Dondi: Add week 9 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and completely fulfilled. Great work!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all on-time, and mostly fulfilled (your shared entry does not have a wiki signature). Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

User talk:ArashLari

2017-11-24T03:18:27Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time but have the following issues:
** The journal entry category is missing.
** The references section is missing.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:18, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the journal page category is missing and there is no wiki signature in the acknowledgments section.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on biology is noted; there is definitely a lot to learn on that side. On the other hand, this degree of depth is what makes for a proper interdisciplinary class. Another perspective is that the biology majors probably feel the same way about the computer science aspect.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted ''4 days'' late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Most “good habit” items are addressed and it was submitted on time.
** The journal page is still missing a category—''add it to your template''.
** There are four (4) listed edits on your individual journal page—marginally sufficient for this week. But there were no summaries entered? You really need to treat these edits like code commits.
* Your electronic notebook has moderate detail—sufficient for the scale of this week’s journal. The narrative style works, makes your process easy to follow.
* Your Acknowledgments and References are OK, except that your wiki signature should be after just your Acknowledgments, not at the very bottom after your References.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
* However, in your answers to the questions, you used manual numbering. Don’t forget the <code>#</code> notation for numbered lists!

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, supplying comments for all 4 of the listed journal edits. The misses are:
** Four edits for an assignment of this size is still quite monolithic; find ways to work more gradually, thus saving more frequently. Build up an internal clock that makes you save your work more often.
** Your journal entry page does not have a category.—note how this would be addressed by adding it to your template—consider doing that.
** Your acknowledgments section is missing the statement that you did all of the work on your own (as specified in [[Week 1]]) as well as your wiki signature.
** Your wiki signature is also missing from your shared journal entry.
* You supplied an electronic notebook with this assignment; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Remember that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…Borat for president!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''name=code''' or '''name=output''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Regarding your chosen shared journal quote, I’d say that sometimes even a month seems slow, and something new comes up every ''day''. That’s why it’s really important to keep up and keep doing things—that’s how you can stay on top of the field.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:20, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your assignment was substantially late. Please let us know if there are any issues we can help you with in terms of assisting you with submitting your work on time.
* You wrote something in the summary field for 0 of 3 saves (0%) in the period of review; this is not counting work that was submitted late.
* You made 9 saves to your Week 2 journal entry, which is barely in the range that would be expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement and your wiki signature (see the [[Week 1]] assignment). This will be required each week.
* You are also completely missing a References section. This section is also required each week and should, at a minimum, have a correctly formatted citation to that week's assignment (APA format).
* As of the the Week 2 deadline, you were also missing most of the required links:
** User to Assignment
** User to journal entry
** Category
** Link from User page to shared journal
** The signature on your shared journal entry.
*** Make sure that your template is up-to-date with the required links and that you are invoking it on your pages, if you have not already done so.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field). Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:58, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* Your user page is missing a snail mail address.
* I don’t see an email from you regarding worries/concerns or additional information.
* Your user page was written out in a single save—not a good habit. Treat wiki pages like code: type them a little at a time, saving often and with a summary.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). All of your wiki links unnecessarily use the external full URL style, and no genuinely external link was noted in your user page.
* No bulleted list was seen in your submission.
* A numbered list was seen (in your shared journal response), but the numbers were written out manually. Use the <code>#</code> symbol to signify a numbered list item.

None of these other items were found in your submission:
* Commented-out content
* Uploaded and linked image
* Uploaded and downloadable file
* Category
* Template
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Link to user page from shared response
* Wiki signature

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:30, 11 September 2017 (PDT)

User talk:Nicolekalcic

2017-11-24T03:15:21Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:53, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are on-time, and almost fulfilled. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified. There is, however, a slight typo in the explanation where ''Homo sapiens'' and ''Saccharomyces cerevisiae'' are referred to as genes instead of species.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:15, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your references were somewhat minimal—you definitely used more sources in this assignment than just the instructions page. Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. It’s good to hear that you are appreciating both the interdisciplinary and the collaborative aspects of the course. It can be challenging, but I think the rewards are commensurate to that challenge.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:17, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:08, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, with the exception of getting all of your work in before the due date; it’s close (last edit at 12:06am) but unfortunately the wiki tells all…
* Your lab notebook is in an easy-to-understand chronological format with good detail for what's there; however, it's a little too focused on just how you and your homework partner coordinated your work—ideally, it also includes details on how you approached the assignment work itself, including what you individually did and how you went about putting the requested content together.
* Your acknowledgments and references were as requested except that the database citations were links alone; all items in a formal references section should use a full citation style.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled except for the aforementioned due date, with edits coming in up to 12:27am.
** Note that the standard library you used here does have a name: Bootstrap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would have as much functionality as they do today.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:32, 10 October 2017 (PDT)

== Week 3 Feedback ==

You certainly were off to a good start, setting up your individual journal page with the right “good habit/best practice” instructions for all individual journal entries. However, you either ran out of time or were quite stuck. Please come to one of our office hours so that we can discuss and try to act upon any difficulties that you might be encountering.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:59, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 20 of 51 saves (39%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks.
* You made 20 saves to your Week 2 journal entry, which is at the high end of the range expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* Actually, the genetic code was cracked closer to 50 years ago--that article is a little dated. The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:36, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases course you are taking right now as your list of upper division courses (since it is the only one). You could include your other upper divisions if you want since you are neither a biology or computer science major.
** We did not receive an e-mail from you regarding your worries/concerns or if there was anything else you wanted us to know. Please send us both an e-mail, even if your answer to both questions is “no”.
** You wrote something in the summary field for 13 of 18 saves, or 72%. We would like to see this approach 100%.
** We would like you to stay away from using “----“ to create sections on your page, and simply use the header system of ==, ===, ====. The plain line should be used sparingly, for special use cases.
** Please use either numbered or bulleted lists when you need to make a list. For example, you used “-“ in your Education section. When you use * or #, MediaWiki will use proper indents and align the lines for you. I did not see an actual numbered list on your page.
** You created your template, and invoked it on your page. However, it seems like you have not added your Week 2 links to the template, but to your user page itself. You should add that information to your template, so that any page where your template is invoked will automatically be updated with that content. The category “Journal Entry” should be added to your template instead for the same reason.
* Including your artwork on the page is great! However, this is a situation where you may want to consider protecting your intellectual property. All content on this wiki is considered to be considered to be released under the Creative Commons Attribution-NonCommercial-ShareAlike license, which means that someone else can redistribute it without your permission, as long as it is attributed to you. You may or may not want this. We can discuss the implications further if you wish.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:40, 12 September 2017 (PDT)''

User talk:Johnllopez616

2017-11-24T03:12:34Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:21, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Well done!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:12, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows excellent detail, effectively presented as bullets.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your observation that the biology content appears to be a challenge across the board is an interesting one. I hope the computer science gets equivalently challenging somehow too!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:10, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are mostly fulfilled, but this time I must really emphasize that the “this week’s journal” format of your user page template is truly showing its disadvantages now that grading has slowed down. “This week’s journal” is already at Week 7, but we needed to grade Week 5. With this time differential, the inconvenience of not having access to the class journals prior to the current week really came to the fore.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten nearly all of the “good habit” tasks down, with 15 listed edits and summary entries for all of them!
** Your inter-page links are still strictly in the “this week” version—as mentioned before, this is not bad to have, but ''also'' have the comprehensive links so that we can jump across weeks very easily.
** The journal entry links on your User page are duplicated up to Week 3.
* Your lab notebook has very good detail, with your headings and links giving it some good organization.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here! Note also your “this week” shared link—ideally, we can access all shared weeks from your user page instead of just the current one.
* Indeed the flip side of the Internet’s current indispensability and importance is now the increased impact of misinformation, hacking, and lost privacy.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** At the time that I reviewed your user page, your assignment links were restricted to “This Week’s Assignment”—not a bad idea in and of itself, but in the long run it will be more useful to have the full list available. I can see now that you have tried to add it, but at this writing you now have redundant versions, one in your template and another directly in the user page. Try to clean things up. You can keep the “This Week’s Assignment” portion, but make sure to also add the comprehensive list (as you have now started to do).
** There are 7 listed edits to your journal page, with comments on all of them. Do treat these like commits: fine-grained, always with a message. For an assignment of this size, I think additional saves would have been appropriate.
* You supplied an electronic notebook with this assignment, with your notes being well-integrated with your answers. Keep this up! You provide some good details in the spirit of openness and reproducibility, the values that we are after here. Always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, and you never know, we have a high-powered enough animation department that Rick & Morty may well visit someday!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. In addition…
* …you also realized that the values after '''seqdna''' in those links do indeed serve as IDs. You also treated URLS themselves as identifiers (and indeed they are sometimes called URIs as well), which is appropriate here.
* Your '''curl'''/'''sed''' command is largely on the money except there is a slight typo in the '''grep''' portion: You only want a leading space before <code>Frame</code>, but not <code>PRE</code>.
* Your references section is generally right, except that it is formatted like code because there is a leading space before each asterisk. Was that intentional? Either way, I think the references will look better without the leading space.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:36, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 5 of 5 saves (100%) in the period of review.
* However, the number of total saves is quite small. We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* Please indicate the ends of your protein sequence with "N-ter" and "C-ter", which is what we use to mark the ends of proteins.
* Your User page was missing the link to the [[Week 2]] assignment. Please add those links to your template and invoke your template on both your User page and individual journal entry pages for the future.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:44, 20 September 2017 (PDT)''

== Week 1 Feedback ==

I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly. We won’t count email misspellings against you 😁

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:36, 11 September 2017 (PDT)

User talk:Simonwro120

2017-11-24T03:11:02Z

Dondi: /* Week 9 Feedback */ Add signature.

==Comments==
Hello everyone, please feel free to leave any comments here! [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 14:17, 4 September 2017 (PDT)
----

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although your individual journal page link appears to be missing from the team template (bottom of page). For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:12, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the '''data/Gene''' web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose <code>primaryIdentifier</code> property looks like an SGD ID (that is, <code>S#########</code>).

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook is detailed and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comments on being a novice are noted—remember that everyone is a novice at everything at some point in their lives, so as long as you keep learning (you call it “re-learning” but that implies that you’ve forgotten what you’ve learned before; I think what you really mean is that you’re feeling like you’ve started over, which is true because you’ve changed majors but you’re learning ''new'' things, not things that you’ve already learned before but have now forgotten).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:27, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:06, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic notebook for this week was a little brief. If you look at your partner's notebook, she included some extra details about the syntax you used. Both of you could have said a little more about your gene in your notebook.
* You made a total of 13 edits to the wiki in the window of review and wrote something in the summary field every time, except for once (oops!)--keep up the good work.
* Don't forget to add your wiki signature to your Acknowledgments statement.
* I want to note that Bootstrap itself is a standard library--you seemed to imply in your shared journal entry that you didn't use it at all and coded your page from scratch, is that the case?

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:21, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Most of your journal was turned in on time—thank you! You did add to your reference list after the due date, at 1:11pm on September 20. Do a re-read/review of your work prior to putting it away, multiple times if needed, to make sure you catch these sooner rather than later.
* You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 17 of the listed journal edits. The misses are:
** Your acknowledgments section is missing the statement that the journal entry is your own work.
** The wiki signature that is supposed to follow that statement got pushed out to after the references section.
* You supplied an electronic notebook with this assignment, organized into headings and bullets—both good ideas. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—for example, what '''curl''' commands did you try out? What search keywords did you use and which search was the most successful? This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—that is one catty-looking dragon ''':)'''
* Your list of links is of decent size and variety, all referencing different types of supporting resources for the page.
* Of your IDs, the first two are known as element IDs and indeed fit the description of identifiers given in class and in the readings. However, '''pre_text''' and '''POST''' do not fit as well, particularly with respect to [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* Your '''curl'''/'''sed''' command is right on, and you make good use of the options available to you, especially '''output=Verbose''' to spell out some key amino acid names.
* Your chosen shared journal quote is one of the more striking ones in the article, and you might recall that when I described a model of a computer during the Week 3 class sessions, I did state that a computer’s activity was indeed centered on a clock. The “clock with benefits” phrase is a cleverer way to capture what goes on, admittedly, rather than my “fetch-decode-execute” cycle (though I think the latter is more descriptive, if drier!).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:26, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 9 of 11 saves (82%) in the period of review. This is very good, but remember, we are aiming for 100%
* The number of total saves on your individual wiki page was 10, which is just within the range of what would be expected for this assignment.
* The only link to your User page from your journal entry was in your wiki signature, and the template/category was added late. The link from your User page to the shared class journal page was also late. In the future, be sure that all the requested links are in your template and invoke them on your pages on time.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see any electronic lab notebook in your journal entry. For this assignment, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as your individual journal entry.
* One small note about your References section: you need to provide a label for the link to the Week 2 assignment.
* Also, for your Acknowledgments section, this exact statement is required each week" "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source" followed by your wiki signature.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:56, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting most of your work on time, though one edit was noticed at 3:42pm on September 5. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 32 edits were made to your user page—a good, gradual pace—but around 7 of those were missing a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* A template was successfully created, but it does not appear to be used anywhere in your submission.

For your shared journal response, no link was seen from your user page to the shared journal page. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:00, 11 September 2017 (PDT)

User talk:Hhinsch

2017-11-24T03:10:17Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Good job!
* The electronic notebook has good detail and is readable and clear in its bulleted format.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:10, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point, and your electronic lab notebook is very thorough and detailed. Great work here!
* Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
* Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
* I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. I didn’t realize that you transferred very recently—it can indeed be a challenging adjustment, but your determination and attitude toward it is certainly healthy so I think it things will work out. At this point you know more about how you’ll be contributing to GRNsight so I hope that this is satisfying as well.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:47, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:08, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
** You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
** You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
** The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
** Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
** The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:39, 10 October 2017 (PDT)'''

=== More Week 4 Feedback ===

* I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your [[Week 7]] version.
* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good.
* You made a total of 26 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* You listed all of your sources in your Reference section, but please provide them in APA format.
* I want to note that Bootstrap itself is a standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:52, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 23 of the listed journal edits.
* You supplied an electronic notebook with this assignment, although more detail is called for. Remember that we maintain such a notebook in the spirit of openness and reproducibility. Always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** In particular, your entries talk about “trying different things,” “a lot of trial and error,” and “just fooling around on Visual Studio Code”—but they don’t say ''what'' different things, or what you tried that didn’t work, or what you meant by “fooling around on Visual Studio Code.” These details make your process more ''open'' and will help readers of your document to not only reproduce what you did, but also to avoid what you’ve already tried that didn’t work.
* Your hack-a-page work certainly fulfilled the instructions—good to see that you had some fun with that.
* Your list of links consists primarily of supporting files for the web page, which is technically correct but there are certainly more kinds beyond that.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* One note regarding your references section: you phrased this similarly to your acknowledgments, using prose descriptive sentences. This approach should only be done in acknowledgments. Formal references are just a list of cited sources (properly cited, of course). Please format your future references sections in that way.
* Your shared journal’s chosen quote is certainly something to be aware of regarding computers, but it seems that these days, especially with the growth of artificial intelligence techniques, people are less and less cognizant of this. Good to know that you gravitated toward this quote!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:55, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 22 of 22 saves (100%) in the period of review, which is excellent, keep up the good work!
* The number of total saves on your individual wiki page was 13, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except in one case where you missed a t > a conversion.
* Your +1 frame had a U instead of an I in one place (not sure how that happened).
* Your +2 fraome had an A instead of an R in one place
* The +3 frame translation was correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:47, 23 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in a list of upper division courses.
** We did not receive an e-mail from you regarding your worries/concerns or if there was anything else you wanted us to know. Please send us both an e-mail, even if your answer to both questions is “no”.
** You wrote something in the summary field for 15 of 18 saves, or 83%. This is very good; we would like to see this approach 100%.
** You created a “redlink” for your Week 2 journal entry, but that is only the first step in creating a new page. The second step is to actually click on the link and edit something, then save. Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones, including the one on the Main course page. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead. Please make this change on the User page and on your template.
** You created a template (<nowiki>[[Template:Hhinsch]]</nowiki>), but did not invoke it on your User page. To invoke it on your user page, you need to include the syntax <nowiki>{{Template:Hhinsch}}</nowiki>. Your template is the page that should include the list of Assignments ([[Week 1]], [[Week 2]], etc.), the list of your individual journal entries ([[Hhinsch_Week_2]], etc.), and the list of shared journal entries ([[Class Journal Week 1]], [[Class Journal Week 2]], etc.), and the category “Journal Entry”. I see that you have created several sub-pages, instead of just creating the one template. Please go back and add the requested content to your main template, invoke your template on your user page and your individual assignment pages, and then we can delete the unused pages. Please let us know if you need assistance.
*** By correcting your template, then the missing link to the shared journal page will be corrected. This is something that will be part of the assignment each week. By using the template, you will save yourself from forgetting and losing points. You can work ahead and create the content for your template for the entire semester, if you wish.
* Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:37, 12 September 2017 (PDT)''

User talk:Simonwro120

2017-11-24T03:02:29Z

Dondi: Add week 9 feedback.

==Comments==
Hello everyone, please feel free to leave any comments here! [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 14:17, 4 September 2017 (PDT)
----

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although your individual journal page link appears to be missing from the team template (bottom of page). For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:12, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the '''data/Gene''' web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose <code>primaryIdentifier</code> property looks like an SGD ID (that is, <code>S#########</code>).

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook is detailed and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comments on being a novice are noted—remember that everyone is a novice at everything at some point in their lives, so as long as you keep learning (you call it “re-learning” but that implies that you’ve forgotten what you’ve learned before; I think what you really mean is that you’re feeling like you’ve started over, which is true because you’ve changed majors but you’re learning ''new'' things, not things that you’ve already learned before but have now forgotten).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:27, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:06, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic notebook for this week was a little brief. If you look at your partner's notebook, she included some extra details about the syntax you used. Both of you could have said a little more about your gene in your notebook.
* You made a total of 13 edits to the wiki in the window of review and wrote something in the summary field every time, except for once (oops!)--keep up the good work.
* Don't forget to add your wiki signature to your Acknowledgments statement.
* I want to note that Bootstrap itself is a standard library--you seemed to imply in your shared journal entry that you didn't use it at all and coded your page from scratch, is that the case?

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:21, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Most of your journal was turned in on time—thank you! You did add to your reference list after the due date, at 1:11pm on September 20. Do a re-read/review of your work prior to putting it away, multiple times if needed, to make sure you catch these sooner rather than later.
* You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 17 of the listed journal edits. The misses are:
** Your acknowledgments section is missing the statement that the journal entry is your own work.
** The wiki signature that is supposed to follow that statement got pushed out to after the references section.
* You supplied an electronic notebook with this assignment, organized into headings and bullets—both good ideas. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—for example, what '''curl''' commands did you try out? What search keywords did you use and which search was the most successful? This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—that is one catty-looking dragon ''':)'''
* Your list of links is of decent size and variety, all referencing different types of supporting resources for the page.
* Of your IDs, the first two are known as element IDs and indeed fit the description of identifiers given in class and in the readings. However, '''pre_text''' and '''POST''' do not fit as well, particularly with respect to [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* Your '''curl'''/'''sed''' command is right on, and you make good use of the options available to you, especially '''output=Verbose''' to spell out some key amino acid names.
* Your chosen shared journal quote is one of the more striking ones in the article, and you might recall that when I described a model of a computer during the Week 3 class sessions, I did state that a computer’s activity was indeed centered on a clock. The “clock with benefits” phrase is a cleverer way to capture what goes on, admittedly, rather than my “fetch-decode-execute” cycle (though I think the latter is more descriptive, if drier!).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:26, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 9 of 11 saves (82%) in the period of review. This is very good, but remember, we are aiming for 100%
* The number of total saves on your individual wiki page was 10, which is just within the range of what would be expected for this assignment.
* The only link to your User page from your journal entry was in your wiki signature, and the template/category was added late. The link from your User page to the shared class journal page was also late. In the future, be sure that all the requested links are in your template and invoke them on your pages on time.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see any electronic lab notebook in your journal entry. For this assignment, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as your individual journal entry.
* One small note about your References section: you need to provide a label for the link to the Week 2 assignment.
* Also, for your Acknowledgments section, this exact statement is required each week" "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source" followed by your wiki signature.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:56, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting most of your work on time, though one edit was noticed at 3:42pm on September 5. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 32 edits were made to your user page—a good, gradual pace—but around 7 of those were missing a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* A template was successfully created, but it does not appear to be used anywhere in your submission.

For your shared journal response, no link was seen from your user page to the shared journal page. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:00, 11 September 2017 (PDT)

User talk:Dbashour

2017-11-24T03:01:15Z

Dondi: Add week 9 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# You forgot to invoke your template on the page, so you were missing the link to the assignment page and your category. The link to your user page was only present in your signature.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* The name of your PowerPoint file was very generic and did not specify your initials or the strain you worked with.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Gln3 transcription factor.
# There was no summary paragraph. In particular, items 3-5 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as the GO term definitions. Please use the full APA format for citations in your references section.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:55, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the '''data/Gene''' web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose <code>primaryIdentifier</code> property looks like an SGD ID (that is, <code>S#########</code>).

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:01, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You replaced all STRAIN references with "dGLN3", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
#* When the instructions say "repeat for all timepoints" you also need to provide the formulas for those because the cell references will change.
# At the top of your notebook, you did not record your strain, nor the number of replicates per timepoint.
# The number of replacements of "NA" was also not recorded.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADH1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. In your dataset, ''NSR1'' has an unadjusted p value < 0.05, but is no longer significant with the corrections. This means that we have some confidence that is is really changing in this experiment, but not as much as some other genes.
#* None of the ''ADH1'' p values are < 0.05, so the Average Log Fold Changes you see are likely just noise.
#* Also note that p values are between 0 and 1, which is why we use the "IF" statement to clear that up. For both genes, you should just report 1 for the Bonferroni p value.
# Your concluding paragraph is not sufficient. You need to summarize the purpose of this analysis, what you did, and your main results, both in terms of the numbers of genes significant and the specific ''NSR1'' and ''ADH1'' values., but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above.
# Instead of having a separate section to report the answers to the questions, it would be better to just answer them at the point in which they appear in the protocol.
# This ''entire'' wiki page is your electronic notebook. The extra section you wrote, more properly belongs in the Acknowledgments section where you describe how you and Zach worked together.
# Finally, you also need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 21:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows a moderate level of detail.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on computer science is noted; I agree with your sentiment that no knowledge is wasted knowledge in this regard. For you, although you are unlikely to write computer code in the future, the hope is that you walk away from this class with enough good exposure to coding that it influences how you think and approach problems, computer-related or not. This is where your exposure to programming and code might make you tackle a problem with greater rigor or precision.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:05, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Punctuality took a hit, with 3 out of 7 listed edits coming after 12:01am, the last one being at 2:43pm
** On the bright side, 7 edits is a good number for this size journal, and you added summary entries to all of them
* Your lab notebook has very good detail, written in chronological log style, with a good focus on content acquisition

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential stealing of information

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in terms of providing feedback on the [[Week 3]] Assignment before I added my feedback on [[Week 2]] :) It looks like you addressed some of the issues I list below in your Week 2 journal entry, but here is the feedback anyway.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 13 of 27 saves (48%) in the period of review. Remember we are aiming for 100%
* However, the number of total saves on your individual wiki page is quite small (only 4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** Also, there appeared to be a spell check problem--"complementary" was given as "contemporary".
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* Your Acknowledgments section is missing your wiki signature.
* In your References section, you need to change the citation to the Week 2 assignment.
* I also note that the links to and from your User page to the journal entry and assignment are formatted as external links. Please be sure to follow the correct syntax for internal wiki links versus external links. Please remove the "Journal entries" category and just keep the "Journal Entry" category.
* My apologies for not getting to discussing "transcriptomes" and "proteomes" in class. We will be picking up those topics in the next week or two. In brief, a transcriptome refers to all of the mRNAs found in a cell at a given time and a protein refers to all of the proteins in a cell at a particular time. The difference is looking at one mRNA or proteina, versus all of them.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:32, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, with your hacked headline fitting with the background image quite nicely!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
* There were a couple of small glitches in your acknowledgments and references: first, the signature should follow your statement about your work in the acknowledgments; in this journal page it appears after the references. And speaking of the references, the assignment reference still says “Week 1” rather than “Week 3.”
* Your shared journal’s chosen quote reflects an unfortunate tendency in computer science, which is the proliferation of jargon. I agree with your sentiments. Here’s hoping that we produce better-trained practitioners who will put more thought into the names that they choose!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:02, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed most of your assignment on time, but we note that you did make some changes after the deadline, including your shared journal assignment and posting questions to myself and Dr. Dionisio’s talk pages.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You included your off-campus residence address on the page to fulfill the requirement for a “snail mail” address. However, to protect your privacy, we suggest that you replace this with the “1 LMU Drive…” general campus address.
** You wrote something in the summary field for 10 of 13 saves, or 77%. We would like to see this approach 100%.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please provide a link to an external website on your User page. This could be to the LMU home page or to some other organization you wish to highlight, for example.
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. Please go back and remove the lines in between, so that the numbered lines appear correctly. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** You created a link to a file you intended to provide on your page, but the file itself was never uploaded to the wiki. Just like with images, it is a two-step process to upload the file and then to link to it on your page.
** Please use the category “Journal Entry” instead of the one you used, including it on your template.
** In a comment, you said you used Eddie Bachoura's page as inspiration. You actually need to say this visibly in your Acknowledgments section; this is the type of thing that we mean needs to go in this section.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

User talk:Emmatyrnauer

2017-11-24T02:41:39Z

Dondi: Add week 9 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. Because your B-H p value computations were incorrect in Week 8, you will need to redo the stem analysis. When you do, come back to edit this page and replace the results shown here with the new ones generated with the correct gene list. When you redo this, also pay attention to the feedback below, making the necessary changes. Your weekly electronic notebook for the project can then link to your Week 10 page, noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did. You do not need to include the "background" section here because it is not really part of anything that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving or opening files, please record the actual filename in your notebook for reference at the point in the protocol where it is mentioned.
# When you discussed why you chose the profile you did, you said the genes were down-regulated, but they are actually up-regulated in that profile.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock. Also, please include their GO IDs.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to cold shock in yeast.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:49, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Thank you!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the last URL that delivers the full data for a single gene. After performing the needed '''esearch''' API calls, you want to make a final '''esummary''' API call in order to get the full dataset for the specific gene whose ID you were able to extract via '''esearch'''.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:41, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.
* Thank you for submitting the assignment on time.
* All required links were present on the page.
You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
#* Since this is recording what you ''did'', the language should be in the ''past'' tense.
#* You replaced all ''STRAIN'' references with "wt", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
# There is a mistake in the Benjamini-Hochberg p value computation.
#* You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula. You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
#* You need to redo this computation. Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''ADA2'' also shows some largish Average Log Fold Changes. But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections. We have less confidence that ''ADA2'' is really changing its expression because of the p value.
# Your summary paragraph is a good description of the flow of work for this week. However, it should draw some more conclusions based on the table of p values and be corrected to interpret the expression of ''NSR1'' and ''ADA2'' above.
#* In particular, do we know if genes are really changing expression, and how do we know it (hint: look at the percent of genes changed at each p value cut-off relative to the cut-off itself, e.g., p < 0.05 = 5%.)
# You included your Acknowledgments and References. However, you should have been more explicit in your Acknowledgments that you directly copied, then modified the Week 8 instructions. You also needed to Acknowledge the source of the data.

Please let me know if you have any questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 15 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively narrated, and your references section thoughtfully includes the multiple sources you consulted for this assignment (although it appears to be missing the baseline reference for [[Week 7]]).
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of carousel is noted as the other “advanced Bootstrap” feature.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Yes, the coding can certainly be challenging and ideally would be given more practice time, but due to our time constraints we have to keep it in the "need-to-know/just-in-time" level. But that’s indeed why we have the mixed partners, so it’s good to hear that this helps you.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 14:32, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
** Your folder name and HTML filename should have been all lowercase letters.
** You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
** Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
** I did not see an actual summary paragraph about your gene.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Don't forget to invoke your template on your individual journal entry page--you were missing the link back to your User page because of it.
* Your electronic lab notebook had a moderate level of detail about what you did, but could have included some of the results as well, gene data and some examples of code that you used for your web page.
* You made a total of 21 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* You had a complete list of references in APA format, but since this is a wiki, please make the URLs hyperlinks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:00, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 18 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' subheading for each section; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…I’m pleasantly surprised that you didn’t encounter any issues with a Facebook image (note how I wouldn’t have known this if you hadn’t indicated as much in your notebook!). Sometimes they limit linkable items from their feeds; good that you weren’t bitten by that here.
* You identified a sufficient number and variety of links correctly, including the '''cgi-bin''' action that does the actual transcription/translation. This appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred—don’t be! Indeed it is by continued exposure that you will gain the foundation you mentioned to increasingly make good use of the functions that are available to you on the command line.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:22, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but you changed 5' and 3' to N-ter and C-ter after the deadline.
* You wrote something in the summary field for 13 of 15 saves (87%) in the period of review, which is very good. Remember, we are aiming for 100%.
* The number of total saves to your Week 2 journal entry before the deadline was 10, which is just within the range for this assignment.
* You were missing the Category "Journal Entry", please add it to your template and invoke your template on future journal entries.
* You were also missing a link back to your User page, except in your wiki signature in the Acknowledgments. Please add this to your template if you have not already and invoke your template in future assignments.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you substituted a G for the second W in the -1 frame.
* Your determination of which frames contained ORFs was correct.
* One note I will make is that you reversed your labeling of the +1, +2, and +3 strands with -1, -2, and -3. It is the convention to call the top 5' to 3' ''DNA'' strand the (+) frames and the bottom 3' to 5' ''DNA'' strand the (-) frames. That is because we normally report gene sequences in the 5' to 3' direction, left to right, and the top-strand would be considered the "mRNA-like" strand because it is in that orientation.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* Not only do experimental descriptions use technical language, they presuppose familiarity with the procedures that those new to the field do not have. We assign this because, like with other fields of endeavor, it is good to take a look at the primary source. I can try to answer any specific questions you have, if you like.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 17:14, 21 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 20 edits were made to your user page—a good, gradual pace—but only around five of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Commented-out content (<code><nowiki></nowiki></code>) was not seen in your submission.
* You created a template correctly, but it is not used.

For your shared journal response, a link to the shared response from your user page was not seen. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:48, 11 September 2017 (PDT)

User talk:Bhamilton18

2017-11-24T02:39:54Z

Dondi: Add week 9 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:00, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are almost fulfilled and on-time. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the last URL that delivers the full data for a single gene. After performing the needed '''esearch''' API calls, you want to make a final '''esummary''' API call in order to get the full dataset for the specific gene whose ID you were able to extract via '''esearch'''.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:39, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the acknowledgments were missing your wiki signature, and the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook is very thorough and detailed.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Unfortunately, the project will be the furthest we will get in the realm of web pages and database integration; hope the biology pace continues to work for you, and we’ll let the other computer science class take care of your interest in those areas.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:22, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:07, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that both your individual and shared journal entries were submitted on time.
* Your electronic lab notebook is excellent, with a good amount of detail. However, it seems like your list-formatting got messed up in places. Make sure that after you save the page, you review it to see whether it displays properly.
* Your frequency of edits is excellent and you wrote something in the summary field 100% of the time--keep up the good work.
* I also want to note that Bootstrap is considered a standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:48, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for 19 out of the 20 listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Note how both issues would be addressed by having them in a template—consider doing that.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment.
* Your hack-a-page work certainly fulfilled the instructions, and really, one can’t go wrong with pugs!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Feeling that “I’m not a natural” can certainly be a challenge, but as you stated, you enjoy puzzles at heart and in many respects computer science in general and programming in particular does share a lot with puzzles. (so do mathematical proofs—I took MATH 248 with Dr. Larson, and she kept referring to the proofs we had to do as “little puzzles”) Keeping hold of that puzzle sensibility can help with “jamming” things into your brain, and of course arriving at a solution to the puzzle certainly helps!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:36, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 23 of 34 saves (68%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 12, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, and +3 translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment, just the answers again. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to write a narrative about your process and keep your electronic lab notebook on the same page as your journal entry.
* One small note about your References section: you need to skip two lines in wiki syntax to get something to appear on a newline.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:41, 23 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You wrote something in the summary field for 18 of 37 saves, or 49%. We would like to see this approach 100%. '''Will Improve'''
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.'''Completed'''
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====. '''Completed'''
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. On the Shared Journal page, you interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.'''Completed'''
** You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in <nowiki>[[Media:filename | visible label]]</nowiki>. It will look neater if you include the label.'''Completed'''
** You included multiple categories on your page; we would prefer to see just the category “Journal Entry” instead of the ones you chose. The value of a category is that everyone is using the same ones to create the Table of Contents page.'''Completed'''
** Another idiosyncrasy of MediaWiki is that if you want something to appear on a new line, you actually have to skip two lines instead of one. If you only skip one, the content on the second line will merge with the previous line. '''Completed'''
* Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:36, 12 September 2017 (PDT)''

User talk:Qlanners

2017-11-24T02:32:26Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:09, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:09, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are almost fulfilled and on-time. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook has good detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly, along with the portions to substitute depending on the desired gene as well as the overall process for going from the gene symbol to the final gene data.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:32, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively presented and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of carousel is noted as the other “advanced Bootstrap” feature.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to hear that you are taking to the interdisciplinary mix well!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 14:29, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:09, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
** Your folder name and HTML filename should have been all lowercase letters.
** You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
** Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
** I did not see an actual summary paragraph about your gene.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good.
* You made a total of 19 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* I would need to confirm with Dr. Dionisio, but what he meant by use of a "standard library" is that a collection of code was available for you to reuse and adapt, i.e., Bootstrap. Just the idea that the computer needed to intepret the HTML code was not what he was getting at with that.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 21 of the listed journal edits.
* You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions—and now we know what you ''really'' want to be doing!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred, and continue to seek more knowledge of the functions that are available to you on the command line.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:21, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for completing your assignment on time.
* You wrote something in the summary field for 19/19 (100%) saves in the period of review--keep up the good work!
* You made 12 saves to your Week 2 page, which is in the expected range for this assignment.
* You hit all the marks for this week's assignment--here is some minor feedback so you can "up your game".
** Since you wrote a program to complete this week's assignment, you should have also included the code, either as a file (if long) or copied directly onto the page.
** How did you know that your code was correct? Did you check your work by doing it by hand? Did you write any tests?
** Your notebook gives a good "free text" description of how you went about constructing your code. To be complete in your documentation, in addition to providing the code, you could have included a set of instructions as to how someone else could run it.
** These three items will contribute to an ''open data ecosystem'' and ''reproducible research'', something that we are aiming towards in this class.
* I don't have a direct answer to the question you posed in your shared journal entry. What I do know is that before there were empirical data to support our current understanding of how the code works, scientists like Francis Crick were coming up with theoretical schemes that included overlapping codons, codons for punctuation, and other things.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:09, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You wrote something in the summary field for 21 of 21 saves, or 100%. Keep up the good work~
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** To protect your privacy, you might want to remove your phone number from this wiki because it is public to the world.
** Under your section on independent research, you use the word “dissertation” in an odd way. Usually this word is reserved for PhD theses. Maybe you meant “dissemination” instead.
** Your new wiki page for this assignment was only a “redlink”. When creating a page, the second step is to click on the link, edit, and save the new page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones, including the one on the Main course page. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please be in the habit of using # to create a numbered list. I saw on the shared journal page you used actual numbers instead. When you use #, the wiki will take care to indent the lines properly.
** You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in <nowiki>[[Media:filename | visible label]]</nowiki>. It will look neater if you include the label.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead. Please make this change.
** You did not use your wiki signature in the required places: to sign your acknowledgments section and your shared journal entry. The wiki signature is <nowiki>~~~~</nowiki>.
** You created and invoked your template and I note that you used the advanced feature to specify weeks. However the name of the template itself is too generic for a wiki shared by our entire class. Please rename your template with your username.
* Thank you for the detailed acknowledgments section; it is exactly what we intended for this section. However, as noted above, in the future, please don’t forget your wiki signature!
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:41, 12 September 2017 (PDT)''

User talk:Mbalducc

2017-11-24T02:29:38Z

Dondi: Add week 9 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* Be attentive to writing something in the summary field '''''every''''' time you make a change to the wiki.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Cin5 transcription factor.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to what is noted in number 2 above.
# The gene list and GO list files were provided (make sure that they have the correct file extensions). However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# The PowerPoint with the screenshots of the stem results was also not found. Without this, I was unable to really review your results. These screenshots will be included in your final presentation and report.
# You did not actually mention which profile you chose until the summary paragraph. This information is critical to your notebook. You reversed the number of genes that belonged to the profile versus expected. The profile you chose has a relatively small number of genes. It would be better to choose one of the profiles with at least 100 genes for the further analysis in the final project.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:54, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are almost fulfilled and on-time. An unusually low subset of the listed submissions in the page’s history have a summary, 9/24.
* The electronic notebook has good detail and is clear in its bulleted form.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly, along with the portions to substitute depending on the desired gene as well as the overall process for going from the gene symbol to the final gene data.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:29, 23 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You provided the formulas that were specific to your dataset. However, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# At the top of the protocol, you recorded your strain, but did not record the number of replicates per timepoint.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and '''HSF1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. NSR1 has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''HSF1'' also shows some largish Average Log Fold Changes. But more importantly, its Benjamini and Hochberg p value is ~0.02, which is significant. So, you can conclude that it '''''is''''' changing expression due to cold shock.
# Your concluding paragraph is pretty good, but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above. Also, you report the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:57, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the signature is missing from the acknowledgments section and the references are somewhat minimal—certainly more material was used in this assignment than just the instructions?
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to see that the out-of-comfort exposure is looking just right for you. It is tricky to strike a balance between sufficient exposure to do something substantive alongside skipping some basics and practice in order to save time, but it's looking like the mix is generally OK for you except for the need for more practice.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:43, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Great work on your individual journal! All “good habit” items are addressed, it was submitted on time, you spaced your work out well (9 edits), and had summary entries for all of them.
* Your electronic notebook has sufficient detail and includes some very specific notes, giving it genuine individuality and keeping it from sounding like it could have been anyone else's process.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential misinformation

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I could record my feedback on [[Week 2]] :) In any event, here is the feedback.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 11 of 19 saves (58%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 16, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, frame translations were correct.
** There was a missing "T" in the +3 frame.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you need to change the citation to the Week 2 assignment.
* For your shared journal, the link from your user page to the shared journal page was missing.
* I also can't really visualize a hypercube; it is something that we can't render in 2D or 3D, I think. The current table form emphasizes how the third nucleotide can be redundant and degenerate. I think the other representation would help to understand how the first or second amino acid could be mutated an change the translation to a related amino acid.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:07, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for 16 out of the 17 listed journal edits.
* You supplied an electronic notebook with this assignment, with the kinds of details that support openness and reproducibility, the values that we are after here. Look to try to answer these questions: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? In that spirit, one portion that could use more detail was the last portion, which you characterized as tricky. Digging into what made something tricky, or what you tried that didn’t work, can be just as helpful to readers of your notebook as talking about what did work.
* Your hack-a-page work certainly fulfilled the instructions, with a nice dash of humor (or is it satire?).
* Your list of links was quite thorough, and of course there are more where those came from.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* Your shared journal chosen quote is actually something I say a lot when I teach computer science courses—learning computer science takes away the “magic” that many people feel when faced with the wonders of technology. The hope, however, is that the knowledge behind the magic actually feels more fulfilling and empowering than the sense of magic itself.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 23 September 2017 (PDT)

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses.
** Please make an explicit statement about your career interests and goals.
** You wrote something in the summary field for 13 of 24 saves, or 54%. We would like to see this approach 100%.
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax, including your name on the Main page.
** You uploaded a file and linked to it on your page, but the name of the file is very generic “Resume.pdf” Someone else in the class could have uploaded a file with the same name and overwritten the file without your knowledge. Now is a good time to get into the habit of using more informative names for your files. Usually this includes your last name and the date, but could include the course, type of assignment, etc. This is especially important when you are posting or sending files via e-mail to another person.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” Please make this change, including it on your template, instead of on the User page itself.
** Also, you did not put the link to the Shared Journal page from your User page. Please include this link on your template as well. For each week, you will need to include links to the actual assignment page, your individual journal page, and the shared journal page from your user page (as well as the category). If you get into the habit of including this on your template, you will only need to edit once and all the pages will reflect the change. You can also go ahead and make your template for the rest of the semester so you will always have this part of the assignment fulfilled.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

User talk:Ebachour

2017-11-24T02:26:10Z

Dondi: /* Week 9 Feedback */ Fix parameter name.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:11, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:11, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are mostly fulfilled except:
** The journal entry category is missing.
** The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook is in narrative form with moderate detail, conveying the process of arriving at the API calls.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
** A generic '''query''' parameter is used for filtering by taxon ID and gene name—although this generally seems to work, particularly when coupled with the '''sort=score''' parameter, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that ''specifically'' asks for a particular taxonID and a particular gene name.
** The derivation of the ID relies on ''screen-scraping''—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:17, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your journal page is missing its category and your references were somewhat minimal, but with incorrect titles! Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on being pushed more into biology than desired is noted, but this level of exposure to the biology side of things is precisely why the class is interdisciplinary. Thus, there ''are'' assignments that require biology to finish. You’ll be amazed at where this deeper learning can lead.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:12, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:56, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Your individual journal was done in a single edit! At least that single edit had a message.
** The journal category is still missing. Template template template so you don’t have to worry about this anymore!
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your acknowledgments and references were as requested except that the headings are swapped, and no signature is supplied with the acknowledgments.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap. I know that you know this, but just pointing out that when answering questions of this nature, don't make any assumptions about what the reader already knows. State as reasonably complete an answer as you can think of. Stating that you used a standard library but not naming it is sort of a gap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would become more like virtual machines than just document viewers.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 10 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I added the feedback on [[Week 2]] :) Nonetheless, here it is:
* While the bulk of your assignment was on time, your signature, Reference section, and template were added after the deadline.
** Your category was completely missing; remember to add it to your template, if you have not already done so.
* You wrote something in the summary field for 5 of 7 saves (71%) in the period of review; remember we are aiming for 100%
* The number of total saves on your individual wiki page was 7, which is a little less than would would have been expected for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except that you converted all t's to u's, which would make it an RNA sequence. Be careful to answer what was asked, which, in this case, was a DNA sequence.
* Your +2 frame had an O instead of a P in one place (a typo?).
* The +1 and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you provided the correct link to the [[Week 2]] Assignment, but forgot to change the label, which still says "Week 1".
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:08, 24 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** Your journal entry page does not have a category—just put this in your template so you don’t forget.
** There are 7 listed edits to your journal page, with comments on 5 of them. Do treat these like commits: fine-grained, always with a message.
* You supplied an electronic notebook with this assignment, but it could use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? For example, you said that the '''sed''' part “took a lot of process of elimination”—what did you try? What did you eliminate? The dead ends are useful to other readers too.
* Your hack-a-page work certainly fulfilled the instructions; the upside-down text is clever. You mentioned ''upsidedowntext.com'' in your notebook, and this should be in the acknowledgments too.
* Your list of links (2 items) was shorter than I would have hoped, given how many there were (and their variety).
* Your list of IDs was more comprehensive, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* As stated, ''upsidedowntext.com'' deserves a mention in your acknowledgments.
* As your shared journal entry and chosen quote indicate, one can certainly spend lots of time “poking around” through algorithms, whether they are what you need or not. Hope the journey itself remains rewarding, as opposed to being a plain time-suck.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed the majority of your assignment on time, but we note that you did make some changes after the deadline.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include a snail mail address on your User Page. You do not have to use your residence address, if it is off-campus. Using the “1 LMU Drive…” general campus address will be sufficient.
** Please make an explicit statement about your career interests and goals.
** As you noted in the summary field for your commit, we did not want you to do the entire assignment in one go. Generally it is a good idea to map out the outline of a page with the headers, then click on the “edit” button next to the header to work on a section individually. Somewhere in the range of 10-20 saves would have been good for this size page.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please organize your page using three levels of headers, ==, ===, and ====; you only had one level, ==, on your page.
** Your numbered list was added after the deadline. One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. You interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** Your “comment out” had incorrect syntax, so it appeared on the page. You need to use <nowiki><!--</nowiki> to open a comment, just like in HTML.
** The animated gif that you chose to upload to your page is fun, but is very distracting for someone to look at who wants to actually read your page. Would you please replace it with a static image?
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using an external link format, please use <nowiki>[[Media:filename | visible label]]</nowiki>.
** The category “Journal Entry” is missing from your page, please include it on your template.
** You acknowledged the sources you used in your Acknowledgments section, but you also need to include the statement “While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.” and include your wiki signature. This will be required every week.
** For the shared journal assignment, you forgot to sign your entry with your wiki signature. This will be a requirement each week as well.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 12 September 2017 (PDT)''

User talk:Kwrigh35

2017-11-24T02:24:39Z

Dondi: /* Week 9 Feedback */ Fix parameter name.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
** A generic '''query''' parameter is used for filtering by taxon ID and gene name—although this generally seems to work, particularly with the '''sort=score''' parameter, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that ''specifically'' asks for a particular taxonID and a particular gene name.
** The derivation of the ID relies on ''screen-scraping''—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:22, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. I agree that without some discomfort, you probably aren’t getting enough of a challenge. So it is good to hear that a little of that is present, but without being way too much to handle.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:26, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
For the second consecutive week, there is no apparent entry from you in the shared class journal. Again, please communicate with us regarding any issues with fulfilling the assignments.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:26, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I could not find any individual journal entry or shared journal entry for you for [[Week 4]]. Please let us know if there are any special circumstances we should know about.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 20 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' section; the subheadings and datestamps (for some of the entries) are good ideas and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…can you imagine what a coup it would be to have them as faculty? Though I suspect that there may be some friction between Watson & Crick and Rosalind Franklin. But the New Caledonian Crow is sure to get along with everyone!
* You identified a sufficient number and variety of links correctly, and also noticed that the links changed to file references when viewed from a local file. This is normal and expected; the links are known as ''relative'' links because their final value is dependent on the source from which they are loaded.
* I did not see any answers to the ID question—please let me know if we need to spend some time with this during office hours.
* For the '''curl'''/'''sed''' exercise, you noticed and used the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. What is missed by the provided answer is that supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “space and spell out” the amino acid letters. Taking a closer look at how the live page operated via the Developer Tools may have helped here.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. Time is indeed one way to get a handle on this specificity. I wrote the wiki pages in a tutorial format, so just going through them with a command line window open next to it might help. If not, I am not aware of Codecademy-style tutorials for the command line off the top of my head, but wouldn’t be surprised if there were something out there.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:11, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 12 of 12 saves (100%) in the period of review--keep up the excellent work!
* However, the number of total saves on your individual wiki page is quite small (only 2). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as the assignment.
* One small note about your References section: a mistake in syntax for the link means that it is not showing up properly on the page. Be sure to proofread your work after you save to ensure you didn't make any syntax errors.
* Thank you for your honest about "skimming" the Nirenberg article. The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:33, 23 September 2017 (PDT)''

== Week 1 Feedback ==

For your individual submission, I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly.

Unfortunately, your shared journal answers could not be found. Please let us know if/when they are available on the wiki. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 11 September 2017 (PDT)

=== Week 1 Feedback Update ===

Your shared journal answers have been reviewed, and they fulfill all of the requested items. Thank you very much!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:25, 13 September 2017 (PDT)

User talk:Kwrigh35

2017-11-24T02:22:42Z

Dondi: Add week 9 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled and on-time.
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
** A generic '''q''' parameter is used for filtering by taxon ID and gene name—although this generally seems to work, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that ''specifically'' asks for a particular taxonID and a particular gene name.
** The derivation of the ID relies on ''screen-scraping''—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:22, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. I agree that without some discomfort, you probably aren’t getting enough of a challenge. So it is good to hear that a little of that is present, but without being way too much to handle.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:26, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
For the second consecutive week, there is no apparent entry from you in the shared class journal. Again, please communicate with us regarding any issues with fulfilling the assignments.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:26, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I could not find any individual journal entry or shared journal entry for you for [[Week 4]]. Please let us know if there are any special circumstances we should know about.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 20 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' section; the subheadings and datestamps (for some of the entries) are good ideas and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…can you imagine what a coup it would be to have them as faculty? Though I suspect that there may be some friction between Watson & Crick and Rosalind Franklin. But the New Caledonian Crow is sure to get along with everyone!
* You identified a sufficient number and variety of links correctly, and also noticed that the links changed to file references when viewed from a local file. This is normal and expected; the links are known as ''relative'' links because their final value is dependent on the source from which they are loaded.
* I did not see any answers to the ID question—please let me know if we need to spend some time with this during office hours.
* For the '''curl'''/'''sed''' exercise, you noticed and used the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. What is missed by the provided answer is that supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “space and spell out” the amino acid letters. Taking a closer look at how the live page operated via the Developer Tools may have helped here.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. Time is indeed one way to get a handle on this specificity. I wrote the wiki pages in a tutorial format, so just going through them with a command line window open next to it might help. If not, I am not aware of Codecademy-style tutorials for the command line off the top of my head, but wouldn’t be surprised if there were something out there.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:11, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 12 of 12 saves (100%) in the period of review--keep up the excellent work!
* However, the number of total saves on your individual wiki page is quite small (only 2). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as the assignment.
* One small note about your References section: a mistake in syntax for the link means that it is not showing up properly on the page. Be sure to proofread your work after you save to ensure you didn't make any syntax errors.
* Thank you for your honest about "skimming" the Nirenberg article. The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:33, 23 September 2017 (PDT)''

== Week 1 Feedback ==

For your individual submission, I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly.

Unfortunately, your shared journal answers could not be found. Please let us know if/when they are available on the wiki. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 11 September 2017 (PDT)

=== Week 1 Feedback Update ===

Your shared journal answers have been reviewed, and they fulfill all of the requested items. Thank you very much!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:25, 13 September 2017 (PDT)

User talk:Cwong34

2017-11-24T02:19:48Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:19, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:04, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are completely fulfilled, and two days early too—great job!
* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
* GRNsight testing is complete with clear feedback on the results.
* The provided '''bash''' script specifies the instructions for arriving at the gene data, including the portions that get substituted based on the desired gene and the final URL that yields the gene data from the assigned source.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:19, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively presented and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to hear that you are taking to the interdisciplinary mix well!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:19, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:24, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:05, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good. I like especially that you noted some HTML syntax in your notebook. You could have included more information about your gene, though.
* You made a total of 25 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 13 October 2017 (PDT)''
I want to note that Bootstrap itself is a standard library.

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The sole miss is:
** Your acknowledgments section is missing the statement that the journal entry is your own work and the wiki signature after that.
* You supplied an electronic notebook with this assignment, with headings to separate out the different sections of the journal. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—as written, it sounds like you got everything right on the first try. Is that true? If that is the case, then great. However it is hard to tell the difference between that or perhaps you did some trial and error first, or perhaps got stuck then asked for help. This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—I’m sure LMU would love to have a Netflix series made about it ''':)'''
* Your list of links (3 items) was shorter than I would have hoped, given how many there were (and their variety).
* Further, '''pre_text''', '''output''', and '''code''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better. As a network resource, '''...cgi-bin/translate...''' can be viewed as an identifier on its own, but I was also hoping that the values after '''seqdna''' in the '''cgi-bin/translate''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text''' (you did notice it as indicated above; including it in your '''curl''' command would have been the next step). This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your chosen shared journal quote (and the sentiment you express after) certainly speaks to how ubiquitous the skill of coding/programming can appear to be. Indeed, I’ve noticed that some proficiency at this is helpful to anyone in almost any profession, because at a minimum it helps us to approach a problem in a constructive, step-by-step manner, whether or not the problem is a computational one.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:58, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but the category was added late. Please add the category to your template, if you haven't already. In the future, you will have taken care of this part of the assignment automatically by invoking your template on your journal entry page.
* You wrote something in the summary field for 10 of 16 saves (63%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks.
* However, the number of total saves to your Week 2 journal entry is quite small (4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* However, you did not actually give the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
* Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement (see the [[Week 1]] assignment) and your wiki signature. This will be required each week.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:54, 20 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 19 edits were made to your user page—a good, gradual pace—but 3 of those were missing a summary message. Please strive to provide a summary all the time, no matter how small the change might be.
* Three levels of headings were requested, but only two were noted in your submission.

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:56, 11 September 2017 (PDT)

User talk:Ebachour

2017-11-24T02:17:44Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:11, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:11, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are mostly fulfilled except:
** The journal entry category is missing.
** The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook is in narrative form with moderate detail, conveying the process of arriving at the API calls.
* GRNsight testing is complete with clear feedback on the results.
* The final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
** A generic '''q''' parameter is used for filtering by taxon ID and gene name—although this generally seems to work, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that ''specifically'' asks for a particular taxonID and a particular gene name.
** The derivation of the ID relies on ''screen-scraping''—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:17, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your journal page is missing its category and your references were somewhat minimal, but with incorrect titles! Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on being pushed more into biology than desired is noted, but this level of exposure to the biology side of things is precisely why the class is interdisciplinary. Thus, there ''are'' assignments that require biology to finish. You’ll be amazed at where this deeper learning can lead.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:12, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:56, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Your individual journal was done in a single edit! At least that single edit had a message.
** The journal category is still missing. Template template template so you don’t have to worry about this anymore!
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your acknowledgments and references were as requested except that the headings are swapped, and no signature is supplied with the acknowledgments.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap. I know that you know this, but just pointing out that when answering questions of this nature, don't make any assumptions about what the reader already knows. State as reasonably complete an answer as you can think of. Stating that you used a standard library but not naming it is sort of a gap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would become more like virtual machines than just document viewers.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 10 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I added the feedback on [[Week 2]] :) Nonetheless, here it is:
* While the bulk of your assignment was on time, your signature, Reference section, and template were added after the deadline.
** Your category was completely missing; remember to add it to your template, if you have not already done so.
* You wrote something in the summary field for 5 of 7 saves (71%) in the period of review; remember we are aiming for 100%
* The number of total saves on your individual wiki page was 7, which is a little less than would would have been expected for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except that you converted all t's to u's, which would make it an RNA sequence. Be careful to answer what was asked, which, in this case, was a DNA sequence.
* Your +2 frame had an O instead of a P in one place (a typo?).
* The +1 and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you provided the correct link to the [[Week 2]] Assignment, but forgot to change the label, which still says "Week 1".
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:08, 24 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** Your journal entry page does not have a category—just put this in your template so you don’t forget.
** There are 7 listed edits to your journal page, with comments on 5 of them. Do treat these like commits: fine-grained, always with a message.
* You supplied an electronic notebook with this assignment, but it could use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? For example, you said that the '''sed''' part “took a lot of process of elimination”—what did you try? What did you eliminate? The dead ends are useful to other readers too.
* Your hack-a-page work certainly fulfilled the instructions; the upside-down text is clever. You mentioned ''upsidedowntext.com'' in your notebook, and this should be in the acknowledgments too.
* Your list of links (2 items) was shorter than I would have hoped, given how many there were (and their variety).
* Your list of IDs was more comprehensive, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* As stated, ''upsidedowntext.com'' deserves a mention in your acknowledgments.
* As your shared journal entry and chosen quote indicate, one can certainly spend lots of time “poking around” through algorithms, whether they are what you need or not. Hope the journey itself remains rewarding, as opposed to being a plain time-suck.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed the majority of your assignment on time, but we note that you did make some changes after the deadline.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include a snail mail address on your User Page. You do not have to use your residence address, if it is off-campus. Using the “1 LMU Drive…” general campus address will be sufficient.
** Please make an explicit statement about your career interests and goals.
** As you noted in the summary field for your commit, we did not want you to do the entire assignment in one go. Generally it is a good idea to map out the outline of a page with the headers, then click on the “edit” button next to the header to work on a section individually. Somewhere in the range of 10-20 saves would have been good for this size page.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please organize your page using three levels of headers, ==, ===, and ====; you only had one level, ==, on your page.
** Your numbered list was added after the deadline. One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. You interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** Your “comment out” had incorrect syntax, so it appeared on the page. You need to use <nowiki><!--</nowiki> to open a comment, just like in HTML.
** The animated gif that you chose to upload to your page is fun, but is very distracting for someone to look at who wants to actually read your page. Would you please replace it with a static image?
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using an external link format, please use <nowiki>[[Media:filename | visible label]]</nowiki>.
** The category “Journal Entry” is missing from your page, please include it on your template.
** You acknowledged the sources you used in your Acknowledgments section, but you also need to include the statement “While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.” and include your wiki signature. This will be required every week.
** For the shared journal assignment, you forgot to sign your entry with your wiki signature. This will be a requirement each week as well.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 12 September 2017 (PDT)''

User talk:Cazinge

2017-11-24T02:12:10Z

Dondi: Add week 9 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:05, 16 November 2017 (PST)''

== Week 9 Feedback ==

* The “good habit” aspects of your individual journal are mostly fulfilled except:
** Acknowledgments/signature and references were added 3-7 days late.
** The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
* The electronic notebook is in brief narrative form but does convey the process of arriving at the API calls.
* GRNsight testing is complete with clear feedback on the results.
* The provided '''bash''' script specifies the instructions for arriving at the gene data, including the portions that get substituted based on the desired gene and the final URL that yields the gene data from the assigned source.

=== Shared Journal ===
Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:12, 23 November 2017 (PST)

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that the electronic notebook is somewhat short on detail (though the brevity is explained with a candidness that is noted). The reference list is thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on your interest primarily being on the computer science side is noted, and that’s fine as long as you continue to retain proficiency in the biology aspect even if the interest level is not that high. When developing software for others, it is important that we acquire a firsthand sense of our user base’s needs, interests, and perspective; this is how we are able to create software to truly fulfill that user base’s needs, as opposed to just checking off requirements without fully appreciating why those requirements are the way they are.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted 8 minutes late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:53, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal landed 19 minutes late…
** …in a single edit! So kind of a double-whammy there. Had you edited more granularly, some edits might have landed on time. At least that single edit had a message.
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

* Most questions and “good habit” points are fulfilled except:
** There is no link from your shared journal back to your user page.
** There is no wiki signature on your shared entry…which is somewhat ironic because you set up the template with a very clear placeholder for the signature 🤔

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment and could still use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, but was the “shmoogle” image made by you? Or did you download it? Note how a thorough notebook (or acknowledgments) would answer this question before it even gets asked.
* Your list of links was quite thorough, including the '''cgi''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted there were other IDs on this page beyond those kinds.
* The note that you did this alone causes some concern. Was this your choice? Beyond your control? If the latter, please notify Dr. Dahlquist or myself in case it needs our inquiry or intervention. Fortunately, this assignment leaned toward the computer science side, toward which you are already comfortable. In other circumstances, not having a partner would have had more negative consequences.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but your template was added late. You also made one small edit past the deadline on your shared journal entry. You were also missing the link from your User page to the [[Week 2]] assignment. Please add these links to your template if you have not done so already.
* You wrote something in the summary field for 4 of 8 saves (50%) in the period of review; since you had only received the feedback about frequency after you submitted this assignment, I am expecting that this number will be improving in subsequent weeks.
** As we discussed in class, you obviously cannot go back to fix this; we will be looking for improvement as the semester goes on. Missing a summary field here and there because you clicked "Save" too fast, is not a big deal. We aim to approach 100%, but anything above 90% is in the acceptable range.
* However, the number of total saves to your Week 2 journal entry is quite small (5). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* We do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. I can go over splicing with you and the alpha helix/beta sheet structures of proteins. I have some 3D models in my office that may be helpful.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses. '''Completed!'''
** Please make an explicit statement about your career interests and goals. '''Completed!'''
** You wrote something in the summary field for 7 of 11 saves, or 64%. We would like to see this approach 100%. '''Will do!'''
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement). '''Completed!'''
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using <nowiki>[[File:filename | visible label]]</nowiki>, please use <nowiki>[[Media:filename | visible label]]</nowiki>. '''Completed!'''
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead of “User Page”. Please make this change. '''Completed!'''
** You did not create or invoke a template on your page. Please see the instructions on the [[Week 1 ]] assignment and let us know if you have questions on how to implement this. '''Completed!'''
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:33, 12 September 2017 (PDT)’’

:: I've updated the page and added all requested features. [[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 09:43, 16 September 2017 (PDT)

Week 9

2017-11-22T08:01:32Z

Dondi: /* One Lifeline Question per Homework Pair */ Fix long-broken link.

'''This journal entry is due on Tuesday, October 31, at 12:01 AM PDT.''' 🎃

== Objectives ==

The objective of this assignment is to lay additional computer science groundwork for the semester’s research project by:
* spending some hands-on time with [https://dondi.github.io/GRNsight GRNsight]
* learning how to work with and explore a web service API and its documentation
* looking at the “favorite gene” pages created by the class

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your template on your journal entry page so that you:
** Link from your journal entry page to this Assignment page.
** Link from your journal entry to your user page.
** Add the "Journal Entry" category to the end of your wiki page.
* Because you have invoked your template on your user page, you should also have a:
** Link from your user page to this Assignment page.
** Link to your journal entry from your user page.
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week, the electronic laboratory notebook you will keep on your individual wiki page retains a crucial role. Because most of this week’s activities are exploratory, it is imperative that these explorations are recorded in sufficient detail so that:
** You do not lose important information that you will need later on.
** You do not unnecessarily repeat something that you already tried this week.
** Readers can get a clear idea of what you tried and didn’t try, what worked and didn’t work.

=== Homework Partners ===

Homework partners for this week are listed below. The particular GRNsight functional area and web service API that you and your partner will work on are also indicated below. You are expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, each partner must submit his or her own work as the individual journal entry (direct copying of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.

* Eddie Azinge, Corinne Wong ([[Media:GRNsight_Testing-D-Pad_Control.pdf|D-Pad Control]]; UniProt)
* Eddie Bachoura, Katie Wright ([[Media:GRNsight_Testing-Viewport_Size.pdf|Viewport Size]]; UniProt)
* Mary Balducci, Quinn Lanners ([[Media:GRNsight_Testing-Edge_Weights_and_Gray_Threshold.pdf|Edge Weights + Gray Threshold]]; NCBI)
* Blair Hamilton, Emma Tyrnauer ([[Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf|Gray Threshold + Zoom]]; NCBI)
* Dina Bashoura, Simon Wroblewski ([[Media:GRNsight_Testing-Edge_Weights_and_Normalization.pdf|Edge Weights + Normalization]]; SGD/YeastMine)
* Hayden Hinsch, John Lopez ([[Media:GRNsight_Testing-Normalization_and_Zoom.pdf|Normalization + Zoom]]; SGD/YeastMine)
* Nicole Kalcic, Arash Lari ([[Media:GRNsight_Testing-Restrict_Viewport_and_Edge_Weights.pdf|Restrict Viewport + Edge Weights]]; Ensembl)
* Antonio Porras, Zach Van Ysseldyk ([[Media:GRNsight_Testing-Restrict_Viewport_and_Zoom.pdf|Restrict Viewport + Zoom]]; Ensembl)

=== Hands-On with GRNsight ===

Each homework pair has been assigned one subset of the [https://github.com/dondi/GRNsight/wiki/Client-Side-Testing-Document GRNsight client-side testing protocol] for the current [http://dondi.github.io/GRNsight/beta.html beta version of GRNsight]. Follow this protocol and report the results of your tests in the electronic journal. Homework partners have one testing subset each so that you can talk to each other about the requested tests, ''but the testing itself should still be done and reported individually'', in the spirit of seeking reproducible results.

# Each feature is to be tested in combination will all three formats that GRNsight can read (Excel workbook, SIF, GraphML). This is already specified in the testing document. Choose one file for each of these formats [https://github.com/dondi/GRNsight/tree/beta/test-files/demo-files from this web page] for use in your tests and specify them in your electronic notebook. In order to have a basis for comparison, homework partners should use the same test files for their individual test sequences.
#* For the Excel workbooks (''.xlsx'') in the linked collection above, click on the file then click ''Download'' to save the file to your computer.
#* For the SIF (''.sif'') and GraphML (''.graphml'') files, click on the file, click on the ''Raw'' button, then either copy-paste or save the resulting file to your computer. The ''.sif'' and ''.graphml'' file extensions are not very well known so the files may end up with ''.txt'' added to them; go ahead and remove that from the files after they are downloaded, confirming to the computer that you know what you’re doing.
#* Alternatively, you can right-click on the ''Raw'' button and choose the ''Save Link as…'' menu item (exact phrasing varies per browser) to jump right to the ''Save'' dialog.
# Each test specifies a sequence of actions to perform, followed by their expected results. Use the latter to determine whether GRNsight passed a particular test. Report the result of each test in your electronic notebook.
#* The version of GRNsight that you are testing is a ''beta'' version, so results that diverge from the expected ones are certainly possible.
#* If the observed result is the same as the expected result, indicate that GRNsight '''passed''' that particular test.
#* If the observed result is ''not'' the same as the expected result, indicate that GRNsight '''failed''' that particular test and ''document what was different''. For many tests, a screenshot will be the most effective way to document this difference, so do not hesitate to supply one.
# If you see any other behavior that appears incorrect, erroneous, or confusing, please report those observations in a section of your electronic notebook as well.
# As always, make sure to document and acknowledge your interactions with your homework partner in the Acknowledgments section of your individual journal.

=== Web Service API Exploration ===

Each homework pair has been assigned one of the four gene-related web services that we have used for the “favorite gene page” assignments (Ensembl, NCBI, UniProt, SGD/YeastMine). Because there are only four such services, two homework pairs will be working on the same service, so if you wish, you may join “fources” (sorry) to explore the same web service together. Still, you must write up your findings ''individually'' in your own respective words.

==== Your Mission ====

For the web service that has been assigned to you, use the information given on this page to discover how to take a gene name/symbol (e.g., ACT1, BRO1, SPT15, etc.) and find your way to its full “data profile” within that service. This process may require multiple web service calls and will involve “reading” web service data formats such as JSON or XML.

Your foundational knowledge for this exercise begins with what you have learned from working with “your favorite gene” and from using the services’ corresponding websites. Furthermore, the final URLs that lead to the full gene data are already known to you: they are in the [[Media:Ajax-starter.zip|''ajax-starter'']] files from the [[Week 7]] assignment. You will want to use a combination of a web browser and '''curl''', with a code-savvy editor like Atom or Visual Studio Code to help make any received data more readable to you.

==== The Deliverable ====

Upon determining how to go from a gene name/symbol to that gene’s individual data record (as shown in the [[Week 7]] [[Media:Ajax-starter.zip|''ajax-starter'']] files), write up this process as a reproducible “recipe” in your electronic journal. In general, this recipe will consist of:
* The URLs to access in order to retrieve the desired data
* Any portions in these URLs that need to be substituted for specific queries, such as the gene name or ID within that web service
* Specific instructions on how to interpret the data returned by each URL so that you can extract exactly the information you need in order to proceed to the next step

This exercise is somewhat unusual in that the work lies in the ''process'' of figuring out how to use the web service. Once the steps are known, actually ''performing'' these steps is quite straightforward. Thus, although the prospect of doing this may be quite intimidating to those who are new to it, please rest assured that the journey itself is the reward here and it is the very open-endedness of this exploration that we’d like you to experience in this exercise.

That said, it is again imperative that you take good notes about the things you try, and their results, so that you don’t go around in circles and eventually narrow down your exploration the the desired set of steps.

==== Per-Service Hints ====

Finally, Dr. Dionisio has some curated notes to help you get started with each web service. These tidbits are chosen based on one or more of the following criteria:
* They ''lead'' to the information you’ll need to work out the entire “recipe,” but not in an obvious, dead-giveaway manner
* They involve information that would otherwise be very difficult to look up or figure out if you don’t have a lot of experience in this area
* They document the final URLs for the gene/protein data, as given in the [[Media:Ajax-starter.zip|''ajax-starter'']] files

Use this information well!

===== UniProt =====
* Relevant documentation:
** http://www.uniprot.org/help/api
** http://www.uniprot.org/help/api_idmapping
** http://www.uniprot.org/help/api_retrieve_entries
* Supplementary websites:
** [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] web page
* Technical information:
** You will encounter ''redirects'' in these web services; web browsers handle this automatically, but if using '''curl''' make sure to add the '''-L''' switch (i.e., '''curl -L '''…)
** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
** UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
* Miscellaneous information:
** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''

===== NCBI =====
* Relevant documentation:
** https://www.ncbi.nlm.nih.gov/gene
** https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
** https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
* Technical information:
** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
** Your URLs will also include brackets ('''<nowiki>[ ]</nowiki>'''), which will need special handling with '''curl''': in these cases, make sure to add the '''-g''' switch (i.e., '''curl -g '''…)
** Your URLs may include spaces; typically, we replace those with ''+'' (plus) symbols
* Miscellaneous information:
** NCBI consists of multiple databases; we care about the ''gene'' database
** NCBI abbreviates the gene name/symbol field as ''sym''
** NCBI stores ''organism''s by their full name, in our case ''Saccharomyces cerevisiae'' (note the space)

===== SGD/YeastMine =====
* Relevant documentation:
** Note that YeastMine is part of an overall project called InterMine, which includes web services for other organisms. At the API level, YeastMine does not have its own documentation. Instead, we use documentation from FlyMine, which is technically equivalent although it stores information about, you guessed it, flies instead of yeast.
** http://iodocs.apps.intermine.org/flymine/docs#/ws-model/GET/model
** http://iodocs.apps.intermine.org/flymine/docs#/ws-data/GET/data/:type
* Technical information:
** The API services for YeastMine all start with https://yeastmine.yeastgenome.org/yeastmine/service —when comparing this to the FlyMine documentation, substitute everything before '''service''' with the URL given here
* Miscellaneous information:
** The data type of interest to us here is ''Gene''
** YeastMine does not abbreviate the gene name symbol field; it spells it out fully as ''symbol''
** Recall how SGD IDs look: they begin with a capital '''S''' followed by nine digits (e.g., “S000003664”) —YeastMine calls this the ''primaryIdentifier''

===== Ensembl =====
* Relevant documentation:
** http://rest.ensembl.org/documentation
** http://rest.ensembl.org/documentation/info/lookup
* Technical information:
** Ensembl requires a ''content-type'' parameter in its URLs; use ''content-type=application/json'' to receive JSON-formatted results
** Ensembl lists our species as ''saccharomyces_cerevisiae'' (all lowercase, with an underscore)

==== One Lifeline Question per Homework Pair ====

Because of the varying levels of quality in the web services’ documentation and the relative unfamiliarity of most of the class with this kind of exercise, the possibility of your getting “stuck” still looms large despite these hints and supplementary information. To accommodate this, each homework pair is allowed to ask Dr. Dionisio ''one lifeline question'' between now and the assignment’s due date. The question must be precise and provide indications that you have done some good-faith exploration on your own. For instance, “How do I access the full protein entry in UniProt given a gene name?” is not a valid lifeline question (obviously, I hope). So choose your question well!

To ask a lifeline question:
# Post the question to [[User_talk:Dondi|Dr. Dionisio’s talk page]] (remember that?)
# Send Dr. Dionisio and Dr. Dahlquist an email notifying us of the question (our wiki does not send notifications for new talk page postings)

Posting the question to the wiki is done in case other students will find the answer helpful for their own explorations. This continues the class’s themes of open science, data sharing, and reproducible results.

== Shared Journal Assignment ==

* Store your journal entry in the shared [[Class Journal Week 9]] page. If this page does not exist yet, go ahead and create it (congratulations on getting in first 👏🏼)
* Link to your journal entry from your user page.
* Link back from the journal entry to your user page.
**'''''NOTE: You can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.'''''
* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

=== Review ===

Look at the gene pages that the class has collectively created via the [[Week 4]] and [[Week 7]] assignments:
* [[Media:act1.zip|ACT1]]
* [[Media:ada2.zip|ADA2]]
* [[Media:Adh1.zip|ADH1]]
* [[Media:Asp1.zip|ASP1]]
* [[Media:BRO1.zip|BRO1]]
* [[Media:CLN1.zip|CLN1]]
* [[Media:hsf1.zip|HSF1]]
* [[Media:Spt15.zip|SPT15]]

=== Decide ===

On the shared journal page:
# Identify two (2) gene pages that you particularly like.
# State what you like about each gene page.
#* Format these as separate answers, for a total of three distinct responses in this week’s shared journal.

[[Category:Assignment]]

Main Page

2017-11-22T06:47:13Z

Dondi: /* Announcements */ Post notice on Week 7.

__NOTOC__
<div style="text-align: center; font-size: 175%">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''BIOL/CMSI 367-01: Biological Databases'''</div>
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Fall 2017</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

* Week 7 feedback has been provided on the user talk pages and corresponding points have been posted to Brightspace. —[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:47, 21 November 2017 (PST)
* Week 8 & 10 feedback has been provided for the Data Analysts on their user talk pages. They should make the requested changes to their individual Week 8 and 10 pages as one of the deliverables for the group project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:54, 20 November 2017 (PST)''
* Feedback on the Team Pages has been recorded on each team member's User Talk pages. Please make the requested changes as part of the [[Week 12]] team assignment. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:44, 16 November 2017 (PST)''

=== Upcoming Seminars ===

* '''Biology Faculty Candidate 1'''
** '''Model Physiology Class:''' Monday, November 20, 10:20 AM, LSB 116.
** '''Research Seminar:''' Tuesday, November 21, 11:30 AM, LSB Auditorium.
** '''Lunch with Students:''' Tuesday, November 22, 12:30-1:30, LSB 2nd Floor Terrace.
* '''Biology Faculty Candidate 2'''
** '''Model Lesson on Animal Physiology:''' Monday, 11/27 at 10:20 AM, LSB 116
** '''Research Seminar:''' Tuesday, 11/28 at 11:30 AM, LSB auditorium
** '''Lunch with Students:''' Tuesday, 11/28 at 12:30-1:30, LSB 2nd floor Terrace
* '''Biology Faculty Candidate 3'''
** '''Model Lesson on Animal Physiology:''' Thursday, 11/30 at 11:30 AM, PER 200
** '''Lunch with Students:''' Thursday, 11/30, 12:30-1:30, LSB 2nd floor Terrace
** '''Research Seminar:''' Friday, 12/1 at 2:00 PM, LSB auditorium


== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="margin-left: auto; margin-right: auto"
| style="padding-right: 1em" | [[User:cazinge|Eddie Azinge]] 
| style="padding-right: 1em" | [[User:Bhamilton18|Blair Hamilton]] 
| style="padding-right: 1em" | [[User:ArashLari|Arash Lari]]
| style="padding-right: 1em" | [[User:Zvanysse|Zachary Van Ysseldyk]]
|-
| style="padding-right: 1em" | [[User:ebachour|Eddie Bachoura]]
| style="padding-right: 1em" | [[User:hhinsch|Hayden Hinsch]]
| style="padding-right: 1em" | [[User:johnllopez616|John Lopez]]
| style="padding-right: 1em" | [[User:Cwong34|Corinne Wong]]
|-
| style="padding-right: 1em" | [[User:Mbalducc|Mary Balducci]]
| style="padding-right: 1em" | [[User:Nicolekalcic|Nicole Kalcic]]
| style="padding-right: 1em" | [[User:Aporras1|Antonio Porras]]
| style="padding-right: 1em" | [[User:kwrigh35|Katie Wright]] 
|-
| style="padding-right: 1em" | [[User:dbashour|Dina Bashoura]]
| style="padding-right: 1em" | [[User:Qlanners|Quinn Lanners]]
| style="padding-right: 1em" | [[User:Emmatyrnauer|Emma Tyrnauer]]
| style="padding-right: 1em" | [[User:Simonwro120|Simon Wroblewski]]
|}

{{ GRNsight Gene Page Project Links }}

== Course Schedule ==

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

* Unless otherwise stated on the schedule, your weekly journals/assignments are due on Tuesdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
* Reading assignments should be completed ''before'' coming to class.
* Dr. Dionisio’s office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support

=== Part 1: Building Blocks (Genetic Code and Web Pages) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 1
| Tuesday<br/>8/29/2017
|
|
* Syllabus walkthrough
* Pairwise interviews and introductions
* Academic Honesty case studies

* Class wiki account: Set up a username and password for this wiki site
| rowspan="2" | [[Week 1]]
(due at 12:01am 9/5)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
!
| Thursday<br/>8/31/2017
| [http://brightspace.lmu.edu Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on Brightspace)

[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)

|
* What is a model?
** Model of a cell/model of a computer
** [[Media:20170831_modeling.pdf | Slides shown in class]]
* Discuss the [[Week 1]] assignment
** Wiki syntax overview
** Lab session to setup User wiki page

{{Course Schedule Divider}}
|-
! 2
| Tuesday<br/>9/5/2017
|DataONE: Data Management PowerPoint (on [http://brightspace.lmu.edu Brightspace])

[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1 ''Genomes 2'']

|
* What is bioinformatics?
* Open Science Ecosystem
* The life cycle of data ([[Media:DataONE_L01_DataManagement.pptx|DataONE slides]])
* Whirlwind tour of genetics
* Other slides are posted on [http://brightspace.lmu.edu Brightspace]

| rowspan="2" | [[Week 2]]
(due at 12:01am 9/12)

[[Class Journal Week 2]]


|-
!
| Thursday<br/>9/7/2017
|
On [http://brightspace.lmu.edu Brightspace]:
* Nirenberg (2004) ''Deciphering the Genetic Code''
* Kaji & Kaji (2004) ''Setting the Record Straight''
* Moody (2004) ''Digital Code of Life'', Ch. 1
* Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]

|
* DNA structure
* Genes as models
* Genetic Code
* Central model of molecular biology
** [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
** This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
** [[Media:BIOL367_Fall2017_GeneticCode-CentralModel.pdf | Genetic Code-Gene Expression Pencil Exercise]]
** [http://brightspace.lmu.edu Slides on Brightspace]

{{Course Schedule Divider}}
|-
! 3
| Tuesday<br/>9/12/2017
| [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol 15(6): e2001414. doi: 10.1371/journal.pbio.2001414]

[http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford (2015) ''What is Code?'']
* Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further

[http://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
| An overview of computers, networks, files, web applications, web services, and databases
* Names, URLs, identifiers
** As applied to biology: genes, species
* “Stuff” on the worldwide web
** Accessing the web on a browser
** “Hacking” a page with browser developer tools
*** The ''Elements'' tab
*** The ''Network'' tab
| rowspan="2" | [[Week 3]]
(due at 12:01am 9/19)

[[Class Journal Week 3]]


|-
!
| Thursday<br/>9/14/2017
| [[Introduction to the Command Line]]

[[Dynamic Text Processing]] (<code>grep</code> and <code>sed</code>)

[[The Web from the Command Line]] (<code>curl</code>)
| Command line lab session
* Hands-on practice
* Accessing the web on the command line
* (partial) [[Week 3]] walkthrough and discussion

{{Course Schedule Divider}}
|-
! 4
| Tuesday<br/>9/19/2017
| 
Sir Tim Berners-Lee, the inventor of the Worldwide Web, is the 2016 recipient of the A. M. Turing Award—computer science’s equivalent of the Nobel Prize:
* [http://amturing.acm.org/award_winners/berners-lee_8087960.cfm Official award citation]
* [https://cacm.acm.org/magazines/2017/6/217732-weaving-the-web/fulltext “Weaving the Web”]—a profile to commemorate the award (watch the embedded video too)
* Of historical interest: Tim Berners-Lee et al, [http://dl.acm.org/citation.cfm?id=179671 The World-Wide Web] (1994), ''Communications of the ACM'', Volume 37, Issue 8, pp. 76–82.
| Web page authoring
* HTML
* Bootstrap
* Web browser development tools
* Discuss [[Week 4]] computer portion
| rowspan="2" | [[Week 4]]
(due at 12:01am 9/26)

[[Class Journal Week 4]]



|-
!
| Thursday<br/>9/21/2017
|

| Introduction to biological databases (part 1)
* Terminology, types, evaluation, four "Gold Standard" databases
* Slides are on [http://brightspace.lmu.edu Brightspace]



{{Course Schedule Divider}}
|-
! 5
| Tuesday<br/>9/26/2017
| [https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]

[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]

| Introduction to biological databases (part 2)
* A closer look at evaluating biological databases (slides on [http://brightspace.lmu.edu Brightspace])
* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]

[[A Quick Relational Database Tour]]
| rowspan="2" | [[Week 5]]
(due at 12:01am 10/3)

[[Class Journal Week 5]]



|-
!
| Thursday<br/>9/28/2017
| For more on the Human Genome Project, see:
* Moody (2004) Chapter 6 (on [http://brightspace.lmu.edu Brightspace])
* [http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]
* [http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]
* [http://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']

|
* [[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
* Human Genome Project to DNA microarrays (slides on [http://brightspace.lmu.edu Brightspace])


{{Course Schedule Divider}}
|-
! 6
| Tuesday<br/>10/3/2017
|
| Database presentations part 1
# Katie and Zach
# Quinn and John
# Eddie A. and Mary B.
# Antonio P. and Arash L.
| rowspan="2" | [[Week 6]]
(due at 12:01am 10/10)

[[Class Journal Week 6]]
|-
!
| Thursday<br/>10/5/2017
|
| Database presentations part 2
# Eddie B. and Emma T.
# Dina B. and Nicole K.
# Hayden and Simon
# Corinne W. and Blair H.

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]

|}

=== Part 2: Going Deeper (Gene Expression Data and Web Services) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 7
| Tuesday<br/>10/10/2017
|
| A little more Bootstrap
* The 12-column grid
* The flex box
| rowspan="2" | [[Week 7]]
(due at 12:01am 10/17)

[[Class Journal Week 7]]



|-
!
| Thursday<br/>10/12/2017
|
| A taste of web services
* Web service case studies
* Web service response formats: JSON, XML, etc.
* A dash of JavaScript

{{Course Schedule Divider}}
|-
! 8
| Tuesday<br/>10/17/2017
| 
[http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]

[http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']

Campbell & Heyer Chapter 4 (on [http://brightspace.lmu.edu on Brightspace])

DeRisi et al. (1997) [http://www.sciencemag.org/content/278/5338/680.full ''Science'' 278: 680-686.]

| Introduction to DNA microarray data
* Experimental design
* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
* Slides on [http://brightspace.lmu.edu Brightspace]
| rowspan="2" | [[Week 8]]
(due at 12:01am 10/24)

[[Class Journal Week 8]]
|-
!
| Thursday<br/>10/19/2017
|
| DNA Microarray Analysis activity part 1
* Statistical analysis of Dahlquist Lab yeast cold shock dataset
* Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]

{{Course Schedule Divider}}
|-
! 9
| Tuesday<br/>10/24/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| An introduction to GRNsight…[http://dondi.github.io/GRNsight/beta.html beta version]
* Overview of features to test
* Talk through GRNsight portion of the assignment

Web services and APIs
* Review what we know so far (particularly [[Media:Architecture-layers.png|this image]])
* Talk through the web service API portion of the assignment
| rowspan="2" | [[Week 9]]
(due at 12:01am 10/31)

[[Class Journal Week 9]]



|-
!
| Thursday<br/>10/26/2017
|
| Case study web service API: https://open.fda.gov/api/

[[How to Read JSON Files]]

[[How to Read XML Files]]
{{Course Schedule Divider}}
|-
! 10
| Tuesday<br/>10/31/2017
| [https://peerj.com/articles/cs-85/ Dahlquist et al. (2016) “GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks”]
| Microarray Data Analysis part 2
* Clustering
* Mathematical Modeling
* Visualization with [http://dondi.github.io/GRNsight/ GRNsight]
* [http://www.opensource.org/ Open Source] review
| rowspan="2" | [[Week 10]]
(due at 12:01am 11/7)

[[Class Journal Week 10]]
|-
!
| Thursday<br/>11/2/2017
|
|
* Continue part 2 of analysis
* Group requests due in class (collected on notecards)
|}

=== Part 3: Integrating for Research (GRNsight integration) ===

{| class="schedule-table"
! #
! Date
! Reading
! Agenda
! Journal
|-
! 11
| Tuesday<br/>11/7/2017
|
| Begin GRNsight Gene Page Project
* Team assignments
* Overview of project
* Work session to create Team wiki pages
| rowspan="2" | [[Week 11]]

(due at 12:01am 11/14)
|-
!
| Thursday<br/>11/9/2017
|
|

Literature searching and annotated bibliographies
* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
* Select microarray papers for journal club

{{Course Schedule Divider}}
|-
! 12
| Tuesday<br/>11/14/2017
|
| First Set of Journal Club Presentations
* Arash and Nicole
* Blair and Zach
* Eddie B. and Simon

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| rowspan="2" | [[Week 12]]

(due at 12:01am 11/21)

|-
!
| Thursday<br/>11/16/2017
|
|
* Presentation by Eddie A. and John
* Status report
* Work session

{{Course Schedule Divider}}
|-
! 13
| Tuesday<br/>11/21/2017
|
| Second Set of Journal Club Presentations
* QAs and Data Analysts

[[Presentation Rubric]]

[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
| '''''No Week 13 assignment'''''

|-
! style="background: #ded" |
| style="background: #efe; border: none" | Thursday<br/>11/23/2017
| style="background: #efe; border: none" |
| style="background: #efe; border: none" | Thanksgiving—no class
| style="background: #efe; border: none" |
{{Course Schedule Divider}}
|-
! 14
| Tuesday<br/>11/28/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 14]]

(due at 12:01am 12/5)
|-
!
| Thursday<br/>11/30/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! 15
| Tuesday<br/>12/5/2017
|
|
* Status report
* Work session
| rowspan="2" | [[Week 15]]

(due at 4:30pm 12/12)
|-
!
| Thursday<br/>12/7/2017
|
|
* Status report
* Work session
{{Course Schedule Divider}}
|-
! style="background: #edd" | F
| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
| style="background: #fee; border: none" |
| style="background: #fee; border: none" | '''Final project presentations 2:00-4:00 PM'''
| style="background: #fee; border: none" |
|-
!
| Friday<br/>12/15/2017 4:30 PM
|
| '''Project deliverables due 4:30 PM'''
|
|}

== Course Information ==

=== Instructors ===

==== [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]] ====
: http://myweb.lmu.edu/kdahlqui
: '''Phone:''' (310) 338-7697
: '''E-mail:''' kdahlquist at lmu dot edu
: '''Office:''' Life Sciences Building 289
: '''Office Hours:''' Mondays 1:00-3:00 PM, Tuesdays and Thursdays 4:00-5:00 PM, and by appointment; I keep a sign-up sheet next to my office door to facilitate appointment-making.

==== [[User:Dondi|John David N. Dionisio, Ph.D.]] ====
: http://dondi.lmu.build
: '''Phone:''' (310) 338-5782
: '''E-mail:''' dondi at lmu dot edu
: '''Office:''' Doolan 106
: '''Office Hours:''' {{Dondi Office Hours}}

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in the Seaver College of Science and Engineering. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with web, database, or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 2:40–3:55pm, Seaver 120 

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is September 1. The withdrawal or credit/no-credit status deadline is November 3.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

# As an LMU Lion, by the [http://studentaffairs.lmu.edu/wellness/lmucares/aboutlmucares/livethelionscode/ Lion’s code], you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students.
# You are responsible for your own learning and for being a good class citizen.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
# You are expected to bring the required materials to each class session.
# Cell phones and other ancillary devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises, provided that you have confirmed with the instructors that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets are being used for other purposes and become distracting to you or others, you will be asked to put them away.
# All students are governed by [http://studentaffairs.lmu.edu/media/studentaffairs/judicialaffairs/documents/lmu-community-standards-2017-18.pdf LMU Community Standards publication]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code.

=== Course Website ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2017/. You will need to have a user account on this wiki to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in the course page on [http://brightspace.lmu.edu Brightspace]. The two cross-listed sections are using the same site, which is listed as "BIOL/CMSI 367-01 Biological Databases". The site will be used for materials that cannot be made public on this wiki, including grades.

=== Email Communication ===

At times we will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email address. Messages sent to the instructors at night or on the weekend will be answered the next school day. Please cc: both instructors on all email messages related to this class.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on this wiki or [http://brightspace.lmu.edu Brightspace] site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Account for this wiki
* [http://www.github.com GitHub account]

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-to-day science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

==== University Core Curriculum ====

This course fulfills the following requirements in the University Core Curriculum:
* Integrations: Interdisciplinary Connections
* Upper Division Information Literacy Flag
* Upper Division Oral Communication Flag

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at [http://brightspace.lmu.edu Brightspace].

Your work in this course will be assessed in five areas:

{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments, individual (10 points each)
| style="text-align: right" | 140
| points
|-
| Weekly electronic lab notebook/journal assignments, shared (3 points each)
| style="text-align: right" | 42
| points
|-
| Oral presentations
| style="text-align: right" | 105
| points 
|-
| Information literacy (additional points added to two journal assignments)
| style="text-align: right" | 24
| points 
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''486'''
| '''points'''
|}

==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow.” For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki. We will create and edit during the semester. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferrable to other applications.

You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every 12:01am on Tuesday Pacific time; consult the schedule for specific due dates for each assignment.
* Each weekly assignment has an individual component and a shared component. You will earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries on your user talk pages.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
* Generally, your journal entries will consist of:
** Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Acknowledgments section (see [[Week 1]] assignment for details)
** References section (see [[Week 1]] assignment for details)
** Shared reflection on your learning, assigned readings, or ethics case studies.

==== Oral Presentations ====

You will give three oral presentations in this course. The first two will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The third will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.'''''

==== Final Group Project ====



In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal, specifically [https://peerj.com/computer-science/ PeerJ Computer Science]. Specific instructions will be posted later in the semester. '''''The Final Written Report cannot be accepted any later than Friday, December 15 at 4:30pm. The Final Written Report must be completed to receive a passing grade in the course.'''''

==== Extra Credit ====

Students may accumulate up to 12.5 points toward their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 2.5 points with up to 5 seminars (12.5 points) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page '''''hard copy''''' of your summary of the seminar '''''in class, within one week''''' of the date of the seminar or they will not count as extra credit.

=== Work Load Expectations ===

In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

=== University Policy on Academic Honesty ===

Loyola Marymount University is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences that can range from receiving no credit for the assignment, failing the class, to expulsion. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including Internet) without properly acknowledging the source. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

[http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf Click here for an online version of the LMU Academic Honesty Policy and Procedures.]

You are required to sign the Academic Honesty Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL367_Fall2017_AcademicHonestyAgreement.pdf|Academic Honesty Agreement]]
* [http://academics.lmu.edu/media/lmuacademics/academichonesty/documents/Academic%20Honesty%20Policy%20FINAL%20Appendices--051116.pdf LMU Academic Honesty Policy and Procedures]
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Media:BIOL367_Fall2017_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]]
** [http://libguides.lmu.edu/content.php?pid=472661&sid=3874648 APA Style for References]
* [http://dondi.lmu.build/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]
* [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

=== Americans with Disabilities Act—Special Accommodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2017/.

User talk:Simonwro120

2017-11-22T06:25:06Z

Dondi: Add week 7 feedback.

==Comments==
Hello everyone, please feel free to leave any comments here! [[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 14:17, 4 September 2017 (PDT)
----

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although your individual journal page link appears to be missing from the team template (bottom of page). For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:12, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook is detailed and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comments on being a novice are noted—remember that everyone is a novice at everything at some point in their lives, so as long as you keep learning (you call it “re-learning” but that implies that you’ve forgotten what you’ve learned before; I think what you really mean is that you’re feeling like you’ve started over, which is true because you’ve changed majors but you’re learning ''new'' things, not things that you’ve already learned before but have now forgotten).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:27, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:06, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic notebook for this week was a little brief. If you look at your partner's notebook, she included some extra details about the syntax you used. Both of you could have said a little more about your gene in your notebook.
* You made a total of 13 edits to the wiki in the window of review and wrote something in the summary field every time, except for once (oops!)--keep up the good work.
* Don't forget to add your wiki signature to your Acknowledgments statement.
* I want to note that Bootstrap itself is a standard library--you seemed to imply in your shared journal entry that you didn't use it at all and coded your page from scratch, is that the case?

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:21, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Most of your journal was turned in on time—thank you! You did add to your reference list after the due date, at 1:11pm on September 20. Do a re-read/review of your work prior to putting it away, multiple times if needed, to make sure you catch these sooner rather than later.
* You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 17 of the listed journal edits. The misses are:
** Your acknowledgments section is missing the statement that the journal entry is your own work.
** The wiki signature that is supposed to follow that statement got pushed out to after the references section.
* You supplied an electronic notebook with this assignment, organized into headings and bullets—both good ideas. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—for example, what '''curl''' commands did you try out? What search keywords did you use and which search was the most successful? This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—that is one catty-looking dragon ''':)'''
* Your list of links is of decent size and variety, all referencing different types of supporting resources for the page.
* Of your IDs, the first two are known as element IDs and indeed fit the description of identifiers given in class and in the readings. However, '''pre_text''' and '''POST''' do not fit as well, particularly with respect to [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* Your '''curl'''/'''sed''' command is right on, and you make good use of the options available to you, especially '''output=Verbose''' to spell out some key amino acid names.
* Your chosen shared journal quote is one of the more striking ones in the article, and you might recall that when I described a model of a computer during the Week 3 class sessions, I did state that a computer’s activity was indeed centered on a clock. The “clock with benefits” phrase is a cleverer way to capture what goes on, admittedly, rather than my “fetch-decode-execute” cycle (though I think the latter is more descriptive, if drier!).

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:26, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 9 of 11 saves (82%) in the period of review. This is very good, but remember, we are aiming for 100%
* The number of total saves on your individual wiki page was 10, which is just within the range of what would be expected for this assignment.
* The only link to your User page from your journal entry was in your wiki signature, and the template/category was added late. The link from your User page to the shared class journal page was also late. In the future, be sure that all the requested links are in your template and invoke them on your pages on time.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see any electronic lab notebook in your journal entry. For this assignment, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as your individual journal entry.
* One small note about your References section: you need to provide a label for the link to the Week 2 assignment.
* Also, for your Acknowledgments section, this exact statement is required each week" "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source" followed by your wiki signature.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:56, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting most of your work on time, though one edit was noticed at 3:42pm on September 5. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 32 edits were made to your user page—a good, gradual pace—but around 7 of those were missing a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* A template was successfully created, but it does not appear to be used anywhere in your submission.

For your shared journal response, no link was seen from your user page to the shared journal page. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:00, 11 September 2017 (PDT)

User talk:Cwong34

2017-11-22T06:19:45Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:19, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:04, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively presented and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen in your page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to hear that you are taking to the interdisciplinary mix well!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:19, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:24, 21 October 2017 (PDT)

== Week 4 Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.

* Your favorite gene page had all of the required syntax and content except as follows:
** You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
** The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
** Make sure to follow the convention of only using lowercase letters in filenames.
** You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
** The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
** Your compare/contrast of content and presentation between the four source databases was a little brief.
** Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:05, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good. I like especially that you noted some HTML syntax in your notebook. You could have included more information about your gene, though.
* You made a total of 25 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:15, 13 October 2017 (PDT)''
I want to note that Bootstrap itself is a standard library.

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The sole miss is:
** Your acknowledgments section is missing the statement that the journal entry is your own work and the wiki signature after that.
* You supplied an electronic notebook with this assignment, with headings to separate out the different sections of the journal. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—as written, it sounds like you got everything right on the first try. Is that true? If that is the case, then great. However it is hard to tell the difference between that or perhaps you did some trial and error first, or perhaps got stuck then asked for help. This aspect improves upon the openness of your process.
* Your hack-a-page work certainly fulfilled the instructions—I’m sure LMU would love to have a Netflix series made about it ''':)'''
* Your list of links (3 items) was shorter than I would have hoped, given how many there were (and their variety).
* Further, '''pre_text''', '''output''', and '''code''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better. As a network resource, '''...cgi-bin/translate...''' can be viewed as an identifier on its own, but I was also hoping that the values after '''seqdna''' in the '''cgi-bin/translate''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text''' (you did notice it as indicated above; including it in your '''curl''' command would have been the next step). This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your chosen shared journal quote (and the sentiment you express after) certainly speaks to how ubiquitous the skill of coding/programming can appear to be. Indeed, I’ve noticed that some proficiency at this is helpful to anyone in almost any profession, because at a minimum it helps us to approach a problem in a constructive, step-by-step manner, whether or not the problem is a computational one.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:58, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but the category was added late. Please add the category to your template, if you haven't already. In the future, you will have taken care of this part of the assignment automatically by invoking your template on your journal entry page.
* You wrote something in the summary field for 10 of 16 saves (63%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks.
* However, the number of total saves to your Week 2 journal entry is quite small (4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* However, you did not actually give the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
* Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement (see the [[Week 1]] assignment) and your wiki signature. This will be required each week.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:54, 20 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 19 edits were made to your user page—a good, gradual pace—but 3 of those were missing a summary message. Please strive to provide a summary all the time, no matter how small the change might be.
* Three levels of headings were requested, but only two were noted in your submission.

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:56, 11 September 2017 (PDT)

User talk:Emmatyrnauer

2017-11-21T22:32:02Z

Dondi: Add week 7 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. Because your B-H p value computations were incorrect in Week 8, you will need to redo the stem analysis. When you do, come back to edit this page and replace the results shown here with the new ones generated with the correct gene list. When you redo this, also pay attention to the feedback below, making the necessary changes. Your weekly electronic notebook for the project can then link to your Week 10 page, noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did. You do not need to include the "background" section here because it is not really part of anything that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving or opening files, please record the actual filename in your notebook for reference at the point in the protocol where it is mentioned.
# When you discussed why you chose the profile you did, you said the genes were down-regulated, but they are actually up-regulated in that profile.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock. Also, please include their GO IDs.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to cold shock in yeast.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:49, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.
* Thank you for submitting the assignment on time.
* All required links were present on the page.
You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
#* Since this is recording what you ''did'', the language should be in the ''past'' tense.
#* You replaced all ''STRAIN'' references with "wt", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
# There is a mistake in the Benjamini-Hochberg p value computation.
#* You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula. You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
#* You need to redo this computation. Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''ADA2'' also shows some largish Average Log Fold Changes. But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections. We have less confidence that ''ADA2'' is really changing its expression because of the p value.
# Your summary paragraph is a good description of the flow of work for this week. However, it should draw some more conclusions based on the table of p values and be corrected to interpret the expression of ''NSR1'' and ''ADA2'' above.
#* In particular, do we know if genes are really changing expression, and how do we know it (hint: look at the percent of genes changed at each p value cut-off relative to the cut-off itself, e.g., p < 0.05 = 5%.)
# You included your Acknowledgments and References. However, you should have been more explicit in your Acknowledgments that you directly copied, then modified the Week 8 instructions. You also needed to Acknowledge the source of the data.

Please let me know if you have any questions.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 15 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively narrated, and your references section thoughtfully includes the multiple sources you consulted for this assignment (although it appears to be missing the baseline reference for [[Week 7]]).
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of carousel is noted as the other “advanced Bootstrap” feature.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Yes, the coding can certainly be challenging and ideally would be given more practice time, but due to our time constraints we have to keep it in the "need-to-know/just-in-time" level. But that’s indeed why we have the mixed partners, so it’s good to hear that this helps you.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 14:32, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
** Your folder name and HTML filename should have been all lowercase letters.
** You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
** Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
** I did not see an actual summary paragraph about your gene.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* Don't forget to invoke your template on your individual journal entry page--you were missing the link back to your User page because of it.
* Your electronic lab notebook had a moderate level of detail about what you did, but could have included some of the results as well, gene data and some examples of code that you used for your web page.
* You made a total of 21 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* You had a complete list of references in APA format, but since this is a wiki, please make the URLs hyperlinks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:00, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 18 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' subheading for each section; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…I’m pleasantly surprised that you didn’t encounter any issues with a Facebook image (note how I wouldn’t have known this if you hadn’t indicated as much in your notebook!). Sometimes they limit linkable items from their feeds; good that you weren’t bitten by that here.
* You identified a sufficient number and variety of links correctly, including the '''cgi-bin''' action that does the actual transcription/translation. This appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred—don’t be! Indeed it is by continued exposure that you will gain the foundation you mentioned to increasingly make good use of the functions that are available to you on the command line.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:22, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but you changed 5' and 3' to N-ter and C-ter after the deadline.
* You wrote something in the summary field for 13 of 15 saves (87%) in the period of review, which is very good. Remember, we are aiming for 100%.
* The number of total saves to your Week 2 journal entry before the deadline was 10, which is just within the range for this assignment.
* You were missing the Category "Journal Entry", please add it to your template and invoke your template on future journal entries.
* You were also missing a link back to your User page, except in your wiki signature in the Acknowledgments. Please add this to your template if you have not already and invoke your template in future assignments.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you substituted a G for the second W in the -1 frame.
* Your determination of which frames contained ORFs was correct.
* One note I will make is that you reversed your labeling of the +1, +2, and +3 strands with -1, -2, and -3. It is the convention to call the top 5' to 3' ''DNA'' strand the (+) frames and the bottom 3' to 5' ''DNA'' strand the (-) frames. That is because we normally report gene sequences in the 5' to 3' direction, left to right, and the top-strand would be considered the "mRNA-like" strand because it is in that orientation.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* Not only do experimental descriptions use technical language, they presuppose familiarity with the procedures that those new to the field do not have. We assign this because, like with other fields of endeavor, it is good to take a look at the primary source. I can try to answer any specific questions you have, if you like.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 17:14, 21 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 20 edits were made to your user page—a good, gradual pace—but only around five of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Commented-out content (<code><nowiki></nowiki></code>) was not seen in your submission.
* You created a template correctly, but it is not used.

For your shared journal response, a link to the shared response from your user page was not seen. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:48, 11 September 2017 (PDT)

User talk:Qlanners

2017-11-21T22:29:19Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:09, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:09, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively presented and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
* All prior web page issues were addressed—great to see that!
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of carousel is noted as the other “advanced Bootstrap” feature.
* Both XML and JSON web API calls were adapted from the starter code as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to hear that you are taking to the interdisciplinary mix well!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 14:29, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:09, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
** Your folder name and HTML filename should have been all lowercase letters.
** You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
** Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
** I did not see an actual summary paragraph about your gene.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good.
* You made a total of 19 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* I would need to confirm with Dr. Dionisio, but what he meant by use of a "standard library" is that a collection of code was available for you to reuse and adapt, i.e., Bootstrap. Just the idea that the computer needed to intepret the HTML code was not what he was getting at with that.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 21 of the listed journal edits.
* You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions—and now we know what you ''really'' want to be doing!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred, and continue to seek more knowledge of the functions that are available to you on the command line.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:21, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for completing your assignment on time.
* You wrote something in the summary field for 19/19 (100%) saves in the period of review--keep up the good work!
* You made 12 saves to your Week 2 page, which is in the expected range for this assignment.
* You hit all the marks for this week's assignment--here is some minor feedback so you can "up your game".
** Since you wrote a program to complete this week's assignment, you should have also included the code, either as a file (if long) or copied directly onto the page.
** How did you know that your code was correct? Did you check your work by doing it by hand? Did you write any tests?
** Your notebook gives a good "free text" description of how you went about constructing your code. To be complete in your documentation, in addition to providing the code, you could have included a set of instructions as to how someone else could run it.
** These three items will contribute to an ''open data ecosystem'' and ''reproducible research'', something that we are aiming towards in this class.
* I don't have a direct answer to the question you posed in your shared journal entry. What I do know is that before there were empirical data to support our current understanding of how the code works, scientists like Francis Crick were coming up with theoretical schemes that included overlapping codons, codons for punctuation, and other things.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:09, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You wrote something in the summary field for 21 of 21 saves, or 100%. Keep up the good work~
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** To protect your privacy, you might want to remove your phone number from this wiki because it is public to the world.
** Under your section on independent research, you use the word “dissertation” in an odd way. Usually this word is reserved for PhD theses. Maybe you meant “dissemination” instead.
** Your new wiki page for this assignment was only a “redlink”. When creating a page, the second step is to click on the link, edit, and save the new page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones, including the one on the Main course page. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please be in the habit of using # to create a numbered list. I saw on the shared journal page you used actual numbers instead. When you use #, the wiki will take care to indent the lines properly.
** You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in <nowiki>[[Media:filename | visible label]]</nowiki>. It will look neater if you include the label.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead. Please make this change.
** You did not use your wiki signature in the required places: to sign your acknowledgments section and your shared journal entry. The wiki signature is <nowiki>~~~~</nowiki>.
** You created and invoked your template and I note that you used the advanced feature to specify weeks. However the name of the template itself is too generic for a wiki shared by our entire class. Please rename your template with your username.
* Thank you for the detailed acknowledgments section; it is exactly what we intended for this section. However, as noted above, in the future, please don’t forget your wiki signature!
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:41, 12 September 2017 (PDT)''

User talk:Zvanysse

2017-11-21T16:54:57Z

Dondi: Add week 7 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:01, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the acknowledgments signature is somewhat misplaced (appearing at the bottom of the page instead of right below) and the references list is quite minimal—certainly you accessed more sources than just the instructions? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
* Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
* I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Thanks for your candor regarding the difficulty level of the biology readings. Not being a biologist, I do occasionally struggle with parts too, and judging by the other shared journal entries it sounds like other classmates have similar challenges. One of our aspirations for the class is to keep everything real and to expose you to genuine current research, and a consequence of that choice is that we get exposed to readings that assume a lot more background that the class has. The good news is that this does seep in somehow, and you will emerge from the class with a lot more new knowledge than it may seem right now.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:54, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:23, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
** You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
** You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
** The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
** Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
** The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:40, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your [[Week 7]] version.
* I want to note that you submitted both your individual and shared journal entries on time.
* Your electronic lab notebook was very brief. While I enjoyed reading more about your gene and why you chose it, the intention behind the notebook is to record the details of your process. You could have included more data about your gene and detail of how you constructed your page, including syntax.
* Be sure to use the APA format for your References section.
* You made a total of 14 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* What is meant by a "standard library" is that a collection of code is available for you to re-use and adapt. In this case, Bootstrap was the standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:11, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Your user page does not have a link to the shared journal.
*** Note how the above issues would be addressed by having them in a template—consider doing that.
** Your acknowledgments section is missing the wiki signature after the statement that the journal entry is your own work.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment, and don’t hesitate to supply details as needed.
* Your hack-a-page work certainly fulfilled the instructions, and thank you for the quick ego boost of seeing my name all over the place ''':)'''
* You certainly identified some links correctly, though all but the last ('''cgi-bin/translate'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin/translate''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Your chosen shared journal quote (and the sentiment you express after) is very much in line with one of my favorite computer science quotes, from Don Knuth I think, which states that programming languages aren’t intended to tell computers what to do, but to tell other programmers what you want the computer to do. This indeed goes into the core notion that programming languages are about communication between people.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 17:43, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* The only link to your User page was found in your wiki signature. The category was also missing. Please add these links to your template and be sure to invoke it subesquent journal entries, if you haven't already.
* You wrote something in the summary field for 0 of 10 saves (0%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks!
* The number of total saves to your Week 2 journal entry is was 8, which is a little lower than what we would expect for this exercise.
* Your translations were correct, except for leaving out one "A" from frame -1 and misreading "W" as "stop" twice. (Intersting side note, in some organisms one of the stop codons ''is'' translated as "W", just not in this exercise.)
* Your determination of which frames contained ORFs was correct.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** The conversion of T to U occurs during ''transcription''. The decoding of the genetic code occurs duing ''translation.''
* Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement (see the [[Week 1]] assignment). This will be required each week.
* In the references section, please make sure you are providing a complete citation in APA format, not just a like to the resource you used.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:19, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* 15 edits were made to your user page—a good, gradual pace—but only around 7 of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
* Three levels of headings were requested, but only two were noted in your submission.
* The Acknowledgments section did not have a wiki signature.
* No References section was seen (recall that, at a minimum, it should have had a link to the [[Week 1]] instructions).

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:55, 11 September 2017 (PDT)

User talk:Hhinsch

2017-11-21T16:47:26Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point, and your electronic lab notebook is very thorough and detailed. Great work here!
* Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
* Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
* I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. I didn’t realize that you transferred very recently—it can indeed be a challenging adjustment, but your determination and attitude toward it is certainly healthy so I think it things will work out. At this point you know more about how you’ll be contributing to GRNsight so I hope that this is satisfying as well.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 08:47, 21 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:08, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your favorite gene page had all of the required syntax and content except as follows:
** The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
** You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
** You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
** The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
** Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
** The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:39, 10 October 2017 (PDT)'''

=== More Week 4 Feedback ===

* I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your [[Week 7]] version.
* I want to note that you submitted both your individual and shared journal entries on time.
* The level of detail in your electronic lab notebook was good.
* You made a total of 26 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
* You listed all of your sources in your Reference section, but please provide them in APA format.
* I want to note that Bootstrap itself is a standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:52, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 23 of the listed journal edits.
* You supplied an electronic notebook with this assignment, although more detail is called for. Remember that we maintain such a notebook in the spirit of openness and reproducibility. Always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** In particular, your entries talk about “trying different things,” “a lot of trial and error,” and “just fooling around on Visual Studio Code”—but they don’t say ''what'' different things, or what you tried that didn’t work, or what you meant by “fooling around on Visual Studio Code.” These details make your process more ''open'' and will help readers of your document to not only reproduce what you did, but also to avoid what you’ve already tried that didn’t work.
* Your hack-a-page work certainly fulfilled the instructions—good to see that you had some fun with that.
* Your list of links consists primarily of supporting files for the web page, which is technically correct but there are certainly more kinds beyond that.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* One note regarding your references section: you phrased this similarly to your acknowledgments, using prose descriptive sentences. This approach should only be done in acknowledgments. Formal references are just a list of cited sources (properly cited, of course). Please format your future references sections in that way.
* Your shared journal’s chosen quote is certainly something to be aware of regarding computers, but it seems that these days, especially with the growth of artificial intelligence techniques, people are less and less cognizant of this. Good to know that you gravitated toward this quote!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:55, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 22 of 22 saves (100%) in the period of review, which is excellent, keep up the good work!
* The number of total saves on your individual wiki page was 13, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except in one case where you missed a t > a conversion.
* Your +1 frame had a U instead of an I in one place (not sure how that happened).
* Your +2 fraome had an A instead of an R in one place
* The +3 frame translation was correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:47, 23 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in a list of upper division courses.
** We did not receive an e-mail from you regarding your worries/concerns or if there was anything else you wanted us to know. Please send us both an e-mail, even if your answer to both questions is “no”.
** You wrote something in the summary field for 15 of 18 saves, or 83%. This is very good; we would like to see this approach 100%.
** You created a “redlink” for your Week 2 journal entry, but that is only the first step in creating a new page. The second step is to actually click on the link and edit something, then save. Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones, including the one on the Main course page. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead. Please make this change on the User page and on your template.
** You created a template (<nowiki>[[Template:Hhinsch]]</nowiki>), but did not invoke it on your User page. To invoke it on your user page, you need to include the syntax <nowiki>{{Template:Hhinsch}}</nowiki>. Your template is the page that should include the list of Assignments ([[Week 1]], [[Week 2]], etc.), the list of your individual journal entries ([[Hhinsch_Week_2]], etc.), and the list of shared journal entries ([[Class Journal Week 1]], [[Class Journal Week 2]], etc.), and the category “Journal Entry”. I see that you have created several sub-pages, instead of just creating the one template. Please go back and add the requested content to your main template, invoke your template on your user page and your individual assignment pages, and then we can delete the unused pages. Please let us know if you need assistance.
*** By correcting your template, then the missing link to the shared journal page will be corrected. This is something that will be part of the assignment each week. By using the template, you will save yourself from forgetting and losing points. You can work ahead and create the content for your template for the entire semester, if you wish.
* Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:37, 12 September 2017 (PDT)''

User talk:Kwrigh35

2017-11-21T07:26:54Z

Dondi: Add week 7 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:59, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook has a moderate level of detail.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. I agree that without some discomfort, you probably aren’t getting enough of a challenge. So it is good to hear that a little of that is present, but without being way too much to handle.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:26, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
For the second consecutive week, there is no apparent entry from you in the shared class journal. Again, please communicate with us regarding any issues with fulfilling the assignments.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:26, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I could not find any individual journal entry or shared journal entry for you for [[Week 4]]. Please let us know if there are any special circumstances we should know about.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:17, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 20 of the listed journal edits.
* You supplied an electronic notebook with this assignment, separated into a ''Notebook'' section; the subheadings and datestamps (for some of the entries) are good ideas and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…can you imagine what a coup it would be to have them as faculty? Though I suspect that there may be some friction between Watson & Crick and Rosalind Franklin. But the New Caledonian Crow is sure to get along with everyone!
* You identified a sufficient number and variety of links correctly, and also noticed that the links changed to file references when viewed from a local file. This is normal and expected; the links are known as ''relative'' links because their final value is dependent on the source from which they are loaded.
* I did not see any answers to the ID question—please let me know if we need to spend some time with this during office hours.
* For the '''curl'''/'''sed''' exercise, you noticed and used the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. What is missed by the provided answer is that supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “space and spell out” the amino acid letters. Taking a closer look at how the live page operated via the Developer Tools may have helped here.
* Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. Time is indeed one way to get a handle on this specificity. I wrote the wiki pages in a tutorial format, so just going through them with a command line window open next to it might help. If not, I am not aware of Codecademy-style tutorials for the command line off the top of my head, but wouldn’t be surprised if there were something out there.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:11, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 12 of 12 saves (100%) in the period of review--keep up the excellent work!
* However, the number of total saves on your individual wiki page is quite small (only 2). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
* Your determination of which frames contained ORFs was correct.
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as the assignment.
* One small note about your References section: a mistake in syntax for the link means that it is not showing up properly on the page. Be sure to proofread your work after you save to ensure you didn't make any syntax errors.
* Thank you for your honest about "skimming" the Nirenberg article. The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:33, 23 September 2017 (PDT)''

== Week 1 Feedback ==

For your individual submission, I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly.

Unfortunately, your shared journal answers could not be found. Please let us know if/when they are available on the wiki. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 11 September 2017 (PDT)

=== Week 1 Feedback Update ===

Your shared journal answers have been reviewed, and they fulfill all of the requested items. Thank you very much!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:25, 13 September 2017 (PDT)

User talk:Bhamilton18

2017-11-21T07:22:32Z

Dondi: Add week 7 feedback.

Talk page of [[User:kwrigh35|Katie Wright]].

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:00, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, but the acknowledgments were missing your wiki signature, and the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook is very thorough and detailed.
* Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ''ASP1'' does not have a hyphen.
* Bootstrap grid layout and flex classes were seen and used appropriately.
* The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
* A second “advanced Bootstrap” feature was not seen.
* The XML and JSON web service calls were adapted as requested.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Unfortunately, the project will be the furthest we will get in the realm of web pages and database integration; hope the biology pace continues to work for you, and we’ll let the other computer science class take care of your interest in those areas.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:22, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:07, 21 October 2017 (PDT)

== Week 4 Partial Feedback ==

I am posting partial feedback on your [[Week 4]] assignment, with respect to your favorite gene page because the [[Week 7]] assignment will build on that.
* Your folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
** However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you ''had'' to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
* You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
* All of the content that was requested was found on the page with the following notes:
** I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
** The link to Ensembl in your references list is broken.
** There are a few typos sprinkled throughout the page
** What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
* Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
* Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
* Otherwise, a clean-looking page with nice section breaks!

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:39, 10 October 2017 (PDT)''

=== More Week 4 Feedback ===

* I want to note that both your individual and shared journal entries were submitted on time.
* Your electronic lab notebook is excellent, with a good amount of detail. However, it seems like your list-formatting got messed up in places. Make sure that after you save the page, you review it to see whether it displays properly.
* Your frequency of edits is excellent and you wrote something in the summary field 100% of the time--keep up the good work.
* I also want to note that Bootstrap is considered a standard library.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:48, 13 October 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for 19 out of the 20 listed journal edits. The misses are:
** I couldn’t find a link from the journal entry back to the user page.
** Your journal entry page does not have a category.
** Note how both issues would be addressed by having them in a template—consider doing that.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? Just expand your coverage to include all aspects of the week’s assignment.
* Your hack-a-page work certainly fulfilled the instructions, and really, one can’t go wrong with pugs!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''method="POST"''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Feeling that “I’m not a natural” can certainly be a challenge, but as you stated, you enjoy puzzles at heart and in many respects computer science in general and programming in particular does share a lot with puzzles. (so do mathematical proofs—I took MATH 248 with Dr. Larson, and she kept referring to the proofs we had to do as “little puzzles”) Keeping hold of that puzzle sensibility can help with “jamming” things into your brain, and of course arriving at a solution to the puzzle certainly helps!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:36, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 23 of 34 saves (68%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 12, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, and +3 translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I saw your separate electronic lab notebook page, but there were no notes for this assignment, just the answers again. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to write a narrative about your process and keep your electronic lab notebook on the same page as your journal entry.
* One small note about your References section: you need to skip two lines in wiki syntax to get something to appear on a newline.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:41, 23 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You wrote something in the summary field for 18 of 37 saves, or 49%. We would like to see this approach 100%. '''Will Improve'''
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.'''Completed'''
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====. '''Completed'''
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. On the Shared Journal page, you interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.'''Completed'''
** You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in <nowiki>[[Media:filename | visible label]]</nowiki>. It will look neater if you include the label.'''Completed'''
** You included multiple categories on your page; we would prefer to see just the category “Journal Entry” instead of the ones you chose. The value of a category is that everyone is using the same ones to create the Table of Contents page.'''Completed'''
** Another idiosyncrasy of MediaWiki is that if you want something to appear on a new line, you actually have to skip two lines instead of one. If you only skip one, the content on the second line will merge with the previous line. '''Completed'''
* Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:36, 12 September 2017 (PDT)''

User talk:Johnllopez616

2017-11-21T07:10:00Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:21, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows excellent detail, effectively presented as bullets.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your observation that the biology content appears to be a challenge across the board is an interesting one. I hope the computer science gets equivalently challenging somehow too!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:10, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are mostly fulfilled, but this time I must really emphasize that the “this week’s journal” format of your user page template is truly showing its disadvantages now that grading has slowed down. “This week’s journal” is already at Week 7, but we needed to grade Week 5. With this time differential, the inconvenience of not having access to the class journals prior to the current week really came to the fore.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:21, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten nearly all of the “good habit” tasks down, with 15 listed edits and summary entries for all of them!
** Your inter-page links are still strictly in the “this week” version—as mentioned before, this is not bad to have, but ''also'' have the comprehensive links so that we can jump across weeks very easily.
** The journal entry links on your User page are duplicated up to Week 3.
* Your lab notebook has very good detail, with your headings and links giving it some good organization.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here! Note also your “this week” shared link—ideally, we can access all shared weeks from your user page instead of just the current one.
* Indeed the flip side of the Internet’s current indispensability and importance is now the increased impact of misinformation, hacking, and lost privacy.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** At the time that I reviewed your user page, your assignment links were restricted to “This Week’s Assignment”—not a bad idea in and of itself, but in the long run it will be more useful to have the full list available. I can see now that you have tried to add it, but at this writing you now have redundant versions, one in your template and another directly in the user page. Try to clean things up. You can keep the “This Week’s Assignment” portion, but make sure to also add the comprehensive list (as you have now started to do).
** There are 7 listed edits to your journal page, with comments on all of them. Do treat these like commits: fine-grained, always with a message. For an assignment of this size, I think additional saves would have been appropriate.
* You supplied an electronic notebook with this assignment, with your notes being well-integrated with your answers. Keep this up! You provide some good details in the spirit of openness and reproducibility, the values that we are after here. Always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, and you never know, we have a high-powered enough animation department that Rick & Morty may well visit someday!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. In addition…
* …you also realized that the values after '''seqdna''' in those links do indeed serve as IDs. You also treated URLS themselves as identifiers (and indeed they are sometimes called URIs as well), which is appropriate here.
* Your '''curl'''/'''sed''' command is largely on the money except there is a slight typo in the '''grep''' portion: You only want a leading space before <code>Frame</code>, but not <code>PRE</code>.
* Your references section is generally right, except that it is formatted like code because there is a leading space before each asterisk. Was that intentional? Either way, I think the references will look better without the leading space.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:36, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 5 of 5 saves (100%) in the period of review.
* However, the number of total saves is quite small. We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* Please indicate the ends of your protein sequence with "N-ter" and "C-ter", which is what we use to mark the ends of proteins.
* Your User page was missing the link to the [[Week 2]] assignment. Please add those links to your template and invoke your template on both your User page and individual journal entry pages for the future.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 11:44, 20 September 2017 (PDT)''

== Week 1 Feedback ==

I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly. We won’t count email misspellings against you 😁

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:36, 11 September 2017 (PDT)

User talk:Dbashour

2017-11-21T07:05:13Z

Dondi: Add week 7 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# You forgot to invoke your template on the page, so you were missing the link to the assignment page and your category. The link to your user page was only present in your signature.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* The name of your PowerPoint file was very generic and did not specify your initials or the strain you worked with.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Gln3 transcription factor.
# There was no summary paragraph. In particular, items 3-5 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as the GO term definitions. Please use the full APA format for citations in your references section.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:55, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You replaced all STRAIN references with "dGLN3", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references.
#* When the instructions say "repeat for all timepoints" you also need to provide the formulas for those because the cell references will change.
# At the top of your notebook, you did not record your strain, nor the number of replicates per timepoint.
# The number of replacements of "NA" was also not recorded.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADH1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. In your dataset, ''NSR1'' has an unadjusted p value < 0.05, but is no longer significant with the corrections. This means that we have some confidence that is is really changing in this experiment, but not as much as some other genes.
#* None of the ''ADH1'' p values are < 0.05, so the Average Log Fold Changes you see are likely just noise.
#* Also note that p values are between 0 and 1, which is why we use the "IF" statement to clear that up. For both genes, you should just report 1 for the Bonferroni p value.
# Your concluding paragraph is not sufficient. You need to summarize the purpose of this analysis, what you did, and your main results, both in terms of the numbers of genes significant and the specific ''NSR1'' and ''ADH1'' values., but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above.
# Instead of having a separate section to report the answers to the questions, it would be better to just answer them at the point in which they appear in the protocol.
# This ''entire'' wiki page is your electronic notebook. The extra section you wrote, more properly belongs in the Acknowledgments section where you describe how you and Zach worked together.
# Finally, you also need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 21:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:06, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows a moderate level of detail.
* All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
* The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
* The JSON API adaptation was not seen.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on computer science is noted; I agree with your sentiment that no knowledge is wasted knowledge in this regard. For you, although you are unlikely to write computer code in the future, the hope is that you walk away from this class with enough good exposure to coding that it influences how you think and approach problems, computer-related or not. This is where your exposure to programming and code might make you tackle a problem with greater rigor or precision.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:05, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Punctuality took a hit, with 3 out of 7 listed edits coming after 12:01am, the last one being at 2:43pm
** On the bright side, 7 edits is a good number for this size journal, and you added summary entries to all of them
* Your lab notebook has very good detail, written in chronological log style, with a good focus on content acquisition

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential stealing of information

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* The HTML filename ended with two ''.html''s (''index.html.html'')—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
* A separate gene summary paragraph was not seen
* The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
* The Ensembl link does not go where it should (in fact it appears to be an error page)
* For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
* Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., ''S. cerevisiae'')
* The [[Week 4]] assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:19, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in terms of providing feedback on the [[Week 3]] Assignment before I added my feedback on [[Week 2]] :) It looks like you addressed some of the issues I list below in your Week 2 journal entry, but here is the feedback anyway.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 13 of 27 saves (48%) in the period of review. Remember we are aiming for 100%
* However, the number of total saves on your individual wiki page is quite small (only 4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Technically, you should have given the complementary ''DNA'' sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
** Also, there appeared to be a spell check problem--"complementary" was given as "contemporary".
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* Your Acknowledgments section is missing your wiki signature.
* In your References section, you need to change the citation to the Week 2 assignment.
* I also note that the links to and from your User page to the journal entry and assignment are formatted as external links. Please be sure to follow the correct syntax for internal wiki links versus external links. Please remove the "Journal entries" category and just keep the "Journal Entry" category.
* My apologies for not getting to discussing "transcriptomes" and "proteomes" in class. We will be picking up those topics in the next week or two. In brief, a transcriptome refers to all of the mRNAs found in a cell at a given time and a protein refers to all of the proteins in a cell at a particular time. The difference is looking at one mRNA or proteina, versus all of them.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:32, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, with your hacked headline fitting with the background image quite nicely!
* Your list of links was quite thorough, including the '''cgi-bin''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
* There were a couple of small glitches in your acknowledgments and references: first, the signature should follow your statement about your work in the acknowledgments; in this journal page it appears after the references. And speaking of the references, the assignment reference still says “Week 1” rather than “Week 3.”
* Your shared journal’s chosen quote reflects an unfortunate tendency in computer science, which is the proliferation of jargon. I agree with your sentiments. Here’s hoping that we produce better-trained practitioners who will put more thought into the names that they choose!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 23:02, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed most of your assignment on time, but we note that you did make some changes after the deadline, including your shared journal assignment and posting questions to myself and Dr. Dionisio’s talk pages.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** You included your off-campus residence address on the page to fulfill the requirement for a “snail mail” address. However, to protect your privacy, we suggest that you replace this with the “1 LMU Drive…” general campus address.
** You wrote something in the summary field for 10 of 13 saves, or 77%. We would like to see this approach 100%.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please provide a link to an external website on your User page. This could be to the LMU home page or to some other organization you wish to highlight, for example.
** You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
** One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. Please go back and remove the lines in between, so that the numbered lines appear correctly. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** You created a link to a file you intended to provide on your page, but the file itself was never uploaded to the wiki. Just like with images, it is a two-step process to upload the file and then to link to it on your page.
** Please use the category “Journal Entry” instead of the one you used, including it on your template.
** In a comment, you said you used Eddie Bachoura's page as inspiration. You actually need to say this visibly in your Acknowledgments section; this is the type of thing that we mean needs to go in this section.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

User talk:ArashLari

2017-11-21T06:53:48Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:52, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the journal page category is missing and there is no wiki signature in the acknowledgments section.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on biology is noted; there is definitely a lot to learn on that side. On the other hand, this degree of depth is what makes for a proper interdisciplinary class. Another perspective is that the biology majors probably feel the same way about the computer science aspect.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted ''4 days'' late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:11, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Most “good habit” items are addressed and it was submitted on time.
** The journal page is still missing a category—''add it to your template''.
** There are four (4) listed edits on your individual journal page—marginally sufficient for this week. But there were no summaries entered? You really need to treat these edits like code commits.
* Your electronic notebook has moderate detail—sufficient for the scale of this week’s journal. The narrative style works, makes your process easy to follow.
* Your Acknowledgments and References are OK, except that your wiki signature should be after just your Acknowledgments, not at the very bottom after your References.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—good job here!
* However, in your answers to the questions, you used manual numbering. Don’t forget the <code>#</code> notation for numbered lists!

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, supplying comments for all 4 of the listed journal edits. The misses are:
** Four edits for an assignment of this size is still quite monolithic; find ways to work more gradually, thus saving more frequently. Build up an internal clock that makes you save your work more often.
** Your journal entry page does not have a category.—note how this would be addressed by adding it to your template—consider doing that.
** Your acknowledgments section is missing the statement that you did all of the work on your own (as specified in [[Week 1]]) as well as your wiki signature.
** Your wiki signature is also missing from your shared journal entry.
* You supplied an electronic notebook with this assignment; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Remember that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions…Borat for president!
* You certainly identified some links correctly, though all but the last ('''cgi-bin'''…) were of the same kind: links to supporting files for the web page. But speaking of '''cgi-bin''', this appears not only as an '''action''' but also in bona fide '''a href''' links, and that ties in to the ID question…
* I was hoping that the values after '''seqdna''' in the '''cgi-bin''' links would be recognized by students as IDs. You listed the '''action''' by itself, which is technically correct, but a finer grain was also present. Further, '''pre_text''' and '''name=code''' or '''name=output''' are not IDs in the same sense that they are used in the assigned reading, particularly [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414 McMurry et al.] IDs closer to the spirit of that reading would have been better.
* For the '''curl'''/'''sed''' exercise, I was hoping that students would notice the '''output''' option that can be provided along with '''pre_text'''. This option controls how the amino acids are displayed. Supplying '''output=Verbose''' to the '''curl''' command would have obviated the need for the '''sed''' commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
* Regarding your chosen shared journal quote, I’d say that sometimes even a month seems slow, and something new comes up every ''day''. That’s why it’s really important to keep up and keep doing things—that’s how you can stay on top of the field.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:20, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Your assignment was substantially late. Please let us know if there are any issues we can help you with in terms of assisting you with submitting your work on time.
* You wrote something in the summary field for 0 of 3 saves (0%) in the period of review; this is not counting work that was submitted late.
* You made 9 saves to your Week 2 journal entry, which is barely in the range that would be expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* One correction to your nomenclature: we do not specify the ends of proteins as 5' and 3', that only refers to DNA and RNA. Instead, the ends of proteins are referred to as N-ter (or amino-terminus) and C-ter (or carboxy-terminus).
* For your References section, please provide the full APA citation style for all of your references and be careful to be using the correct link syntax.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* In your Acknowledgments section, you left out the required statement and your wiki signature (see the [[Week 1]] assignment). This will be required each week.
* You are also completely missing a References section. This section is also required each week and should, at a minimum, have a correctly formatted citation to that week's assignment (APA format).
* As of the the Week 2 deadline, you were also missing most of the required links:
** User to Assignment
** User to journal entry
** Category
** Link from User page to shared journal
** The signature on your shared journal entry.
*** Make sure that your template is up-to-date with the required links and that you are invoking it on your pages, if you have not already done so.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field). Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:58, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* Your user page is missing a snail mail address.
* I don’t see an email from you regarding worries/concerns or additional information.
* Your user page was written out in a single save—not a good habit. Treat wiki pages like code: type them a little at a time, saving often and with a summary.
* There is a difference between internal wiki links (double bracket) and external links (single bracket). All of your wiki links unnecessarily use the external full URL style, and no genuinely external link was noted in your user page.
* No bulleted list was seen in your submission.
* A numbered list was seen (in your shared journal response), but the numbers were written out manually. Use the <code>#</code> symbol to signify a numbered list item.

None of these other items were found in your submission:
* Commented-out content
* Uploaded and linked image
* Uploaded and downloadable file
* Category
* Template
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Link to user page from shared response
* Wiki signature

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:30, 11 September 2017 (PDT)

User talk:Cazinge

2017-11-21T06:46:39Z

Dondi: /* Week 7 Feedback */ Punctuation.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although the team template [[Template:Gene hAPI]] is somewhat underpopulated—continue reading to get further ideas on what can go there.

For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:05, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that the electronic notebook is somewhat short on detail (though the brevity is explained with a candidness that is noted). The reference list is thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on your interest primarily being on the computer science side is noted, and that’s fine as long as you continue to retain proficiency in the biology aspect even if the interest level is not that high. When developing software for others, it is important that we acquire a firsthand sense of our user base’s needs, interests, and perspective; this is how we are able to create software to truly fulfill that user base’s needs, as opposed to just checking off requirements without fully appreciating why those requirements are the way they are.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:04, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, except that the entry itself was submitted 8 minutes late.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:53, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal landed 19 minutes late…
** …in a single edit! So kind of a double-whammy there. Had you edited more granularly, some edits might have landed on time. At least that single edit had a message.
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

* Most questions and “good habit” points are fulfilled except:
** There is no link from your shared journal back to your user page.
** There is no wiki signature on your shared entry…which is somewhat ironic because you set up the template with a very clear placeholder for the signature 🤔

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
* You supplied an electronic notebook with this assignment, but it only covered the '''sed''' portion of the assignment and could still use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
* Your hack-a-page work certainly fulfilled the instructions, but was the “shmoogle” image made by you? Or did you download it? Note how a thorough notebook (or acknowledgments) would answer this question before it even gets asked.
* Your list of links was quite thorough, including the '''cgi''' links for the reading frames, which I was hoping that students would catch. However…
* …I was also hoping that the values after '''seqdna''' in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted there were other IDs on this page beyond those kinds.
* The note that you did this alone causes some concern. Was this your choice? Beyond your control? If the latter, please notify Dr. Dahlquist or myself in case it needs our inquiry or intervention. Fortunately, this assignment leaned toward the computer science side, toward which you are already comfortable. In other circumstances, not having a partner would have had more negative consequences.
* Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 2 Feedback ==

* Your turned in most of your assignment on time, but your template was added late. You also made one small edit past the deadline on your shared journal entry. You were also missing the link from your User page to the [[Week 2]] assignment. Please add these links to your template if you have not done so already.
* You wrote something in the summary field for 4 of 8 saves (50%) in the period of review; since you had only received the feedback about frequency after you submitted this assignment, I am expecting that this number will be improving in subsequent weeks.
** As we discussed in class, you obviously cannot go back to fix this; we will be looking for improvement as the semester goes on. Missing a summary field here and there because you clicked "Save" too fast, is not a big deal. We aim to approach 100%, but anything above 90% is in the acceptable range.
* However, the number of total saves to your Week 2 journal entry is quite small (5). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
* Your complementary DNA sequence was correct.
* Your translations were correct.
* Your determination of which frames contained ORFs was correct.
* We do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
* I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source. I can go over splicing with you and the alpha helix/beta sheet structures of proteins. I have some 3D models in my office that may be helpful.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 12:03, 20 September 2017 (PDT)''

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses. '''Completed!'''
** Please make an explicit statement about your career interests and goals. '''Completed!'''
** You wrote something in the summary field for 7 of 11 saves, or 64%. We would like to see this approach 100%. '''Will do!'''
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement). '''Completed!'''
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using <nowiki>[[File:filename | visible label]]</nowiki>, please use <nowiki>[[Media:filename | visible label]]</nowiki>. '''Completed!'''
** You included a category on your page, but we would prefer you to use the category “Journal Entry” instead of “User Page”. Please make this change. '''Completed!'''
** You did not create or invoke a template on your page. Please see the instructions on the [[Week 1 ]] assignment and let us know if you have questions on how to implement this. '''Completed!'''
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:33, 12 September 2017 (PDT)’’

:: I've updated the page and added all requested features. [[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 09:43, 16 September 2017 (PDT)

User talk:Aporras1

2017-11-21T06:45:20Z

Dondi: /* Week 7 Feedback */ Punctuation.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

User talk:Mbalducc

2017-11-21T06:44:22Z

Dondi: /* Week 7 Feedback */ Punctuation.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* Be attentive to writing something in the summary field '''''every''''' time you make a change to the wiki.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Cin5 transcription factor.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to what is noted in number 2 above.
# The gene list and GO list files were provided (make sure that they have the correct file extensions). However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# The PowerPoint with the screenshots of the stem results was also not found. Without this, I was unable to really review your results. These screenshots will be included in your final presentation and report.
# You did not actually mention which profile you chose until the summary paragraph. This information is critical to your notebook. You reversed the number of genes that belonged to the profile versus expected. The profile you chose has a relatively small number of genes. It would be better to choose one of the profiles with at least 100 genes for the further analysis in the final project.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:54, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You provided the formulas that were specific to your dataset. However, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# At the top of the protocol, you recorded your strain, but did not record the number of replicates per timepoint.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and '''HSF1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. NSR1 has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''HSF1'' also shows some largish Average Log Fold Changes. But more importantly, its Benjamini and Hochberg p value is ~0.02, which is significant. So, you can conclude that it '''''is''''' changing expression due to cold shock.
# Your concluding paragraph is pretty good, but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above. Also, you report the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:57, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the signature is missing from the acknowledgments section and the references are somewhat minimal—certainly more material was used in this assignment than just the instructions?
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene.
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
** The gene page does not have its own references section (separate from the one in your individual journal page).
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to see that the out-of-comfort exposure is looking just right for you. It is tricky to strike a balance between sufficient exposure to do something substantive alongside skipping some basics and practice in order to save time, but it's looking like the mix is generally OK for you except for the need for more practice.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:43, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Great work on your individual journal! All “good habit” items are addressed, it was submitted on time, you spaced your work out well (9 edits), and had summary entries for all of them.
* Your electronic notebook has sufficient detail and includes some very specific notes, giving it genuine individuality and keeping it from sounding like it could have been anyone else's process.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential misinformation

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I could record my feedback on [[Week 2]] :) In any event, here is the feedback.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 11 of 19 saves (58%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 16, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, frame translations were correct.
** There was a missing "T" in the +3 frame.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you need to change the citation to the Week 2 assignment.
* For your shared journal, the link from your user page to the shared journal page was missing.
* I also can't really visualize a hypercube; it is something that we can't render in 2D or 3D, I think. The current table form emphasizes how the third nucleotide can be redundant and degenerate. I think the other representation would help to understand how the first or second amino acid could be mutated an change the translation to a related amino acid.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:07, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for 16 out of the 17 listed journal edits.
* You supplied an electronic notebook with this assignment, with the kinds of details that support openness and reproducibility, the values that we are after here. Look to try to answer these questions: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? In that spirit, one portion that could use more detail was the last portion, which you characterized as tricky. Digging into what made something tricky, or what you tried that didn’t work, can be just as helpful to readers of your notebook as talking about what did work.
* Your hack-a-page work certainly fulfilled the instructions, with a nice dash of humor (or is it satire?).
* Your list of links was quite thorough, and of course there are more where those came from.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* Your shared journal chosen quote is actually something I say a lot when I teach computer science courses—learning computer science takes away the “magic” that many people feel when faced with the wonders of technology. The hope, however, is that the knowledge behind the magic actually feels more fulfilling and empowering than the sense of magic itself.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 23 September 2017 (PDT)

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses.
** Please make an explicit statement about your career interests and goals.
** You wrote something in the summary field for 13 of 24 saves, or 54%. We would like to see this approach 100%.
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax, including your name on the Main page.
** You uploaded a file and linked to it on your page, but the name of the file is very generic “Resume.pdf” Someone else in the class could have uploaded a file with the same name and overwritten the file without your knowledge. Now is a good time to get into the habit of using more informative names for your files. Usually this includes your last name and the date, but could include the course, type of assignment, etc. This is especially important when you are posting or sending files via e-mail to another person.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” Please make this change, including it on your template, instead of on the User page itself.
** Also, you did not put the link to the Shared Journal page from your User page. Please include this link on your template as well. For each week, you will need to include links to the actual assignment page, your individual journal page, and the shared journal page from your user page (as well as the category). If you get into the habit of including this on your template, you will only need to edit once and all the pages will reflect the change. You can also go ahead and make your template for the rest of the semester so you will always have this part of the assignment fulfilled.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

User talk:Mbalducc

2017-11-21T06:43:40Z

Dondi: Add week 7 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project. Thank you for submitting the assignment on time and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is insufficient.
#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did.
#* If there were issues with running the protocol, those need to be noted.
#* When you talk about saving files, please record the actual filename in your notebook for reference.
#* Be attentive to writing something in the summary field '''''every''''' time you make a change to the wiki.
# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Cin5 transcription factor.
# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to what is noted in number 2 above.
# The gene list and GO list files were provided (make sure that they have the correct file extensions). However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# The PowerPoint with the screenshots of the stem results was also not found. Without this, I was unable to really review your results. These screenshots will be included in your final presentation and report.
# You did not actually mention which profile you chose until the summary paragraph. This information is critical to your notebook. You reversed the number of genes that belonged to the profile versus expected. The profile you chose has a relatively small number of genes. It would be better to choose one of the profiles with at least 100 genes for the further analysis in the final project.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used as well as each of the GO term definitions, not just the general Gene Ontology site.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:29, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

You covered some of the basics for your team page, but some specifically requested items were missing:
* You need to add a category with your team's name, i.e., "Page Desiigner".
* Please remove the category "Assignment" from your page/template.
* Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? You did include the [[Template:GRNsight Gene Page Project Links]], but then redundantly added a separate list of guild links.
* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:54, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made some changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Since this is recording what you did, the language should be in the past tense.
#* You provided the formulas that were specific to your dataset. However, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# At the top of the protocol, you recorded your strain, but did not record the number of replicates per timepoint.
# You reported the Average Log Fold Changes and p values for ''NSR1'' and '''HSF1'', but your interpretation needs work.
#* The Average Log Fold Change at each time point tells us the magnitude of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. NSR1 has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
#* ''HSF1'' also shows some largish Average Log Fold Changes. But more importantly, its Benjamini and Hochberg p value is ~0.02, which is significant. So, you can conclude that it '''''is''''' changing expression due to cold shock.
# Your concluding paragraph is pretty good, but you need to include the interpretation of the p values of ''NSR1'' and ''HSF1'' as noted above. Also, you report the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:57, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point, except that the signature is missing from the acknowledgments section and the references are somewhat minimal—certainly more material was used in this assignment than just the instructions?
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene
** The gene page does not have its own acknowledgments section (separate from the one in your individual journal page)
** The gene page does not have its own references section (separate from the one in your individual journal page)
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page
* The use of collapse is noted as one of the requested “advanced Bootstrap” features
* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential
* The XML and JSON API calls were adapted correctly

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Good to see that the out-of-comfort exposure is looking just right for you. It is tricky to strike a balance between sufficient exposure to do something substantive alongside skipping some basics and practice in order to save time, but it's looking like the mix is generally OK for you except for the need for more practice.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:43, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:00, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* Great work on your individual journal! All “good habit” items are addressed, it was submitted on time, you spaced your work out well (9 edits), and had summary entries for all of them.
* Your electronic notebook has sufficient detail and includes some very specific notes, giving it genuine individuality and keeping it from sounding like it could have been anyone else's process.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap
** Indeed the flip side of widespread information availability is the loss of privacy and potential misinformation

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
* Your link to the ''.zip'' file used <code>File:</code> rather than <code>Media:</code>; although this was not directly stipulated in the instructions, note that <code>Media:</code> leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
* A separate gene summary paragraph was not seen
* The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
* The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
* The web page was supposed to have its own Acknowledgments and References too

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:39, 2 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I could record my feedback on [[Week 2]] :) In any event, here is the feedback.
* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 11 of 19 saves (58%) in the period of review. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 16, which is in the range of what was expected for this assignment.
* Your complementary DNA sequence was correct.
* Your +1, +2, frame translations were correct.
** There was a missing "T" in the +3 frame.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you need to change the citation to the Week 2 assignment.
* For your shared journal, the link from your user page to the shared journal page was missing.
* I also can't really visualize a hypercube; it is something that we can't render in 2D or 3D, I think. The current table form emphasizes how the third nucleotide can be redundant and degenerate. I think the other representation would help to understand how the first or second amino acid could be mutated an change the translation to a related amino acid.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:07, 23 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for 16 out of the 17 listed journal edits.
* You supplied an electronic notebook with this assignment, with the kinds of details that support openness and reproducibility, the values that we are after here. Look to try to answer these questions: Can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? In that spirit, one portion that could use more detail was the last portion, which you characterized as tricky. Digging into what made something tricky, or what you tried that didn’t work, can be just as helpful to readers of your notebook as talking about what did work.
* Your hack-a-page work certainly fulfilled the instructions, with a nice dash of humor (or is it satire?).
* Your list of links was quite thorough, and of course there are more where those came from.
* You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
* Your shared journal chosen quote is actually something I say a lot when I teach computer science courses—learning computer science takes away the “magic” that many people feel when faced with the wonders of technology. The hope, however, is that the knowledge behind the magic actually feels more fulfilling and empowering than the sense of magic itself.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:53, 23 September 2017 (PDT)

== Week 1 Feedback ==

* Thank you for completing the assignment on time.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses.
** Please make an explicit statement about your career interests and goals.
** You wrote something in the summary field for 13 of 24 saves, or 54%. We would like to see this approach 100%.
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax, including your name on the Main page.
** You uploaded a file and linked to it on your page, but the name of the file is very generic “Resume.pdf” Someone else in the class could have uploaded a file with the same name and overwritten the file without your knowledge. Now is a good time to get into the habit of using more informative names for your files. Usually this includes your last name and the date, but could include the course, type of assignment, etc. This is especially important when you are posting or sending files via e-mail to another person.
** You included a category on your page, but we would prefer you to use the category “Journal Entry” Please make this change, including it on your template, instead of on the User page itself.
** Also, you did not put the link to the Shared Journal page from your User page. Please include this link on your template as well. For each week, you will need to include links to the actual assignment page, your individual journal page, and the shared journal page from your user page (as well as the category). If you get into the habit of including this on your template, you will only need to edit once and all the pages will reflect the change. You can also go ahead and make your template for the rest of the semester so you will always have this part of the assignment fulfilled.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:35, 12 September 2017 (PDT)''

User talk:Aporras1

2017-11-21T06:25:37Z

Dondi: Move week 7 to appear below week 8 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly
* The use of collapse is noted as one of the requested “advanced Bootstrap” features
* The use of card is noted as the other “advanced Bootstrap” feature, though it’s usage does not really maximize its potential
* The XML and JSON API calls were adapted correctly

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

User talk:Aporras1

2017-11-21T06:23:39Z

Dondi: Add week 7 feedback.

== Week 10 Feedback ==

I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
# You did not report the definitions of your 6 GO terms.
# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
# In your References section, you need to cite the stem software that you used. Eventually when you look up the GO term definitions, you will need to cite those pages as well.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
* Nearly all prior web page issues were addressed except:
** Title tag was not modified to match gene
** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly
* The use of collapse is noted as one of the requested “advanced Bootstrap” features
* The use of card is noted as the other “advanced Bootstrap” feature, though it’s usage does not really maximize its potential
* The XML and JSON API calls were adapted correctly

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:23, 20 November 2017 (PST)

== Week 8 Feedback ==

I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.

* Thank you for submitting the assignment on time.
* All required links were present on the page.

You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
# Your computations and Excel file were correct--no corrections are needed there.
# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 19:22, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
** But on a positive note, all 35 listed edits had a summary entry—keep that up!
** Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
* Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
* Your references were as requested except that the Week 3 reference was not updated to Week 4.

=== Shared Journal ===

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was not seen
* The displayed Ensembl gene ID doesn't match the ID in the link
* The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
* Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:20, 2 October 2017 (PDT)

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
* Your journal entry page does not have a category—just put this in your template so you don’t forget.
* You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
** Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
* Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines ''were'' about domesticated teddy bear hamsters!
* You listed a good number of links for a variety of resource types, so that works out nicely.
* Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
* Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—''limits''. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 15:46, 24 September 2017 (PDT)

== Week 2 Feedback ==

* Thank you for turning in your assignment on time.
* You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
* The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
* Your +1, +2, and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 23:40, 23 September 2017 (PDT)''

== Week 1 Feedback ==

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:
* I don’t see an email from you regarding worries/concerns or additional information.
* You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:
* Acknowledgments
* References

For your shared journal response, the following requested items were not seen:
* Link to shared response from user page
* Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 21:42, 11 September 2017 (PDT)

User talk:Nicolekalcic

2017-11-21T06:17:29Z

Dondi: Add week 7 feedback.

User talk:Ebachour

2017-11-21T06:12:30Z

Dondi: Add week 7 feedback.

== Week 11 Team Page Feedback (to address in Week 12) ==

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. For [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
* A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, [[Template:GRNsight Gene Page Project Links]] has already been created for you—won’t that be useful to have on your page as well?)
Note how these items are very similar to the content that can be seen on our own [[Main Page]]—this is not a coincidence.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 00:11, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:11, 16 November 2017 (PST)''

== Week 7 Feedback ==

* The “good habit” aspects of your individual journal are mostly on point except that your journal page is missing its category and your references were somewhat minimal, but with incorrect titles! Your electronic notebook has a moderate amount of detail.
* Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
* Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
* The use of tooltips is noted as the other “advanced Bootstrap” feature.
* The XML and JSON API calls were adapted correctly.

=== Shared Journal ===
Questions and “good habit” aspects are fulfilled, all on-time. Your comment on being pushed more into biology than desired is noted, but this level of exposure to the biology side of things is precisely why the class is interdisciplinary. Thus, there ''are'' assignments that require biology to finish. You’ll be amazed at where this deeper learning can lead.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:12, 20 November 2017 (PST)

== Week 5 Feedback ==

(work in progress)

=== Shared Journal ===
Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 18:56, 21 October 2017 (PDT)

== Week 4 Feedback ==

=== Individual Journal ===

* You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
** Your individual journal was done in a single edit! At least that single edit had a message.
** The journal category is still missing. Template template template so you don’t have to worry about this anymore!
* Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
* Your acknowledgments and references were as requested except that the headings are swapped, and no signature is supplied with the acknowledgments.

=== Shared Journal ===

* All questions and “good habit” points are fulfilled—once again, good job!
** Note that the standard library you used here does have a name: Bootstrap. I know that you know this, but just pointing out that when answering questions of this nature, don't make any assumptions about what the reader already knows. State as reasonably complete an answer as you can think of. Stating that you used a standard library but not naming it is sort of a gap.
** Indeed I don’t think Sir Berners-Lee anticipated that web browsers would become more like virtual machines than just document viewers.

=== Web Page ===

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:
* Filenames and title element weren’t customized to your chosen gene
* A separate gene summary paragraph was seen, and contains appropriate content for a summary
* The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
* Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
* Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
* The references section is always meant to look like a formal citation; supplying just a link is insufficient

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:25, 10 October 2017 (PDT)

== Week 2 Feedback ==

I see that Dr. Dionisio "lapped" me in providing feedback on [[Week 3]] before I added the feedback on [[Week 2]] :) Nonetheless, here it is:
* While the bulk of your assignment was on time, your signature, Reference section, and template were added after the deadline.
** Your category was completely missing; remember to add it to your template, if you have not already done so.
* You wrote something in the summary field for 5 of 7 saves (71%) in the period of review; remember we are aiming for 100%
* The number of total saves on your individual wiki page was 7, which is a little less than would would have been expected for this assignment.
* The link from your User page to the [[Week 2]] assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
* Your complementary DNA sequence was correct, except that you converted all t's to u's, which would make it an RNA sequence. Be careful to answer what was asked, which, in this case, was a DNA sequence.
* Your +2 frame had an O instead of a P in one place (a typo?).
* The +1 and +3 frame translations were correct.
* However, the -1, -2, and -3 frame translations were completely incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
* Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
* One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
* Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
* I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
* In your References section, you provided the correct link to the [[Week 2]] Assignment, but forgot to change the label, which still says "Week 1".
* The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 00:08, 24 September 2017 (PDT)''

== Week 3 Feedback ==

* Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
** Your journal entry page does not have a category—just put this in your template so you don’t forget.
** There are 7 listed edits to your journal page, with comments on 5 of them. Do treat these like commits: fine-grained, always with a message.
* You supplied an electronic notebook with this assignment, but it could use additional detail. Openness and reproducibility are the values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? For example, you said that the '''sed''' part “took a lot of process of elimination”—what did you try? What did you eliminate? The dead ends are useful to other readers too.
* Your hack-a-page work certainly fulfilled the instructions; the upside-down text is clever. You mentioned ''upsidedowntext.com'' in your notebook, and this should be in the acknowledgments too.
* Your list of links (2 items) was shorter than I would have hoped, given how many there were (and their variety).
* Your list of IDs was more comprehensive, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
* As stated, ''upsidedowntext.com'' deserves a mention in your acknowledgments.
* As your shared journal entry and chosen quote indicate, one can certainly spend lots of time “poking around” through algorithms, whether they are what you need or not. Hope the journey itself remains rewarding, as opposed to being a plain time-suck.

—[[User:Dondi|Dondi]] ([[User talk:Dondi|talk]]) 22:44, 23 September 2017 (PDT)

== Week 1 Feedback ==

* You completed the majority of your assignment on time, but we note that you did make some changes after the deadline.
* You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the [[Week 3]] journal deadline.
** Please include a snail mail address on your User Page. You do not have to use your residence address, if it is off-campus. Using the “1 LMU Drive…” general campus address will be sufficient.
** Please make an explicit statement about your career interests and goals.
** As you noted in the summary field for your commit, we did not want you to do the entire assignment in one go. Generally it is a good idea to map out the outline of a page with the headers, then click on the “edit” button next to the header to work on a section individually. Somewhere in the range of 10-20 saves would have been good for this size page.
** Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
** Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.
** Please organize your page using three levels of headers, ==, ===, and ====; you only had one level, ==, on your page.
** Your numbered list was added after the deadline. One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. You interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
** Your “comment out” had incorrect syntax, so it appeared on the page. You need to use <nowiki><!--</nowiki> to open a comment, just like in HTML.
** The animated gif that you chose to upload to your page is fun, but is very distracting for someone to look at who wants to actually read your page. Would you please replace it with a static image?
** You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using an external link format, please use <nowiki>[[Media:filename | visible label]]</nowiki>.
** The category “Journal Entry” is missing from your page, please include it on your template.
** You acknowledged the sources you used in your Acknowledgments section, but you also need to include the statement “While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.” and include your wiki signature. This will be required every week.
** For the shared journal assignment, you forgot to sign your entry with your wiki signature. This will be a requirement each week as well.
* I answered your question on my [[User_talk:Kdahlquist | User talk page]].

''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 13:34, 12 September 2017 (PDT)''