User talk:Dbashour - Revision history

Kdahlquist: note about input file

2017-12-09T18:58:46Z

note about input file

Dondi: Add week 9 feedback.

2017-11-24T03:01:15Z

Add week 9 feedback.

Dondi: Add week 7 feedback.

2017-11-21T07:05:13Z

Add week 7 feedback.

Kdahlquist: provided Week 10 feedback

2017-11-17T06:55:33Z

provided Week 10 feedback

Kdahlquist: /* Week 8 Feedback */ fix syntax

2017-11-17T05:56:44Z

‎Week 8 Feedback: fix syntax

Kdahlquist: added Week 8 feedback

2017-11-17T05:29:38Z

added Week 8 feedback

Kdahlquist: /* Week 11 Team Page Feedback (to address in Week 12) */ add more week 11 feedback

2017-11-16T22:06:52Z

‎Week 11 Team Page Feedback (to address in Week 12): add more week 11 feedback

Dondi: Add team page feedback.

2017-11-16T08:20:05Z

Add team page feedback.

Dondi: Add week 5 shared journal feedback.

2017-10-22T02:00:51Z

Add week 5 shared journal feedback.

Dondi: Provide Week 4 feedback.

2017-10-03T06:19:29Z

Provide Week 4 feedback.

← Older revision		Revision as of 18:58, 9 December 2017
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		+	Dina, here is the new input file: [[Media:15-genes 32-edges team-hAPI Sigmoid estimation.xlsx \| 15-genes 32-edges team-hAPI Sigmoid estimation.xlsx]]. I ran it on one of the computers in Seaver 120 in the back row. I left a note with your name on it there. The files will be on the T: drive in a folder called "Dina". I reduced the size of the network for the input file because it was too big. You will need to view it in GRNsight again. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 10:58, 9 December 2017 (PST)''
		+
	== Week 10 Feedback ==		== Week 10 Feedback ==

← Older revision		Revision as of 03:01, 24 November 2017
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	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:55, 16 November 2017 (PST)''		''— [[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 ==		== Week 8 Feedback ==

← Older revision		Revision as of 07:05, 21 November 2017
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	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 14:06, 16 November 2017 (PST)''		''— [[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 ==		== Week 5 Feedback ==

← Older revision		Revision as of 06:55, 17 November 2017
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		+	== 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 ==		== Week 8 Feedback ==

@@ Line 15: / Line 15: @@
 # 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.
+# 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.

← Older revision		Revision as of 05:29, 17 November 2017
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		+	== 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) ==		== Week 11 Team Page Feedback (to address in Week 12) ==

← Older revision		Revision as of 22:06, 16 November 2017
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	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 00:20, 16 November 2017 (PST)		—[[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 5 Feedback ==		== Week 5 Feedback ==

← Older revision		Revision as of 08:20, 16 November 2017
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		+	== 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)
		+
	== Week 5 Feedback ==		== Week 5 Feedback ==

← Older revision		Revision as of 02:00, 22 October 2017
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		+	== 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 ==		== Week 4 Feedback ==

← Older revision		Revision as of 06:19, 3 October 2017
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		+	== 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 ==		== Week 2 Feedback ==