Week 12 - Revision history

Kdahlquist: /* Presentation Prep: Individual Journal Pages */ add link to LibGuide

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‎Presentation Prep: Individual Journal Pages: add link to LibGuide

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Dondi: /* Data Analyst and Quality Assurance: Prepare a Journal Club Presentation for Your Assigned Paper */ Restore bio-centric version of 10-terms instruction.

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‎Data Analyst and Quality Assurance: Prepare a Journal Club Presentation for Your Assigned Paper: Restore bio-centric version of 10-terms instruction.

Kdahlquist: /* Coders and Designer: Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock */ fix title

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‎Coders and Designer: Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock: fix title

Kdahlquist: /* Whole Team Journal Assignment: Creating a Team Wiki Page */ modified instructions

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‎Whole Team Journal Assignment: Creating a Team Wiki Page: modified instructions

Kdahlquist: /* Coders and Designer: Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock */ note about what to do and electronic lab notebook.

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‎Coders and Designer: Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock: note about what to do and electronic lab notebook.

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‎QA's and Data Analysts: Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock: removed old content

Kdahlquist: /* Coders and Designer: Prepare a Journal Club Presentation for Your Assigned Paper */ modified the what should be included in the presentation

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‎Coders and Designer: Prepare a Journal Club Presentation for Your Assigned Paper: modified the what should be included in the presentation

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{{Under_Construction}}

'''This journal entry is due on Tuesday, November 21, at 12:01 PST.''' ''(Monday night/Tuesday morning)''

== Overview ==

The objectives of this week's exercise is based on your assigned role on your team:
* Everyone will contribute to [[Week_11#Team_Journal_Assignment | revising your team's home page.]]
* QA's and Data Analysts will prepare their journal club presentations on an instructor-approved paper from the [[Week 11]] annotated bibliography assignment and deliver the presentation itself on Tuesday, November 21.
* Coders (and Designer) will complete Milestones 0 through 3 and begin Milestone 4 as detailed on the [[Coder]] page.

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 5 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.
* The journal club presentation (whether delivered on November 14 or 21) will be worth a total of 40 points.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 12" (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.
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.''' Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week, your '''''electronic laboratory notebook''''' will be modified to fit the assignment that is specific to your role on your team.

=== Team Membership ===

The project groups and roles are are:
# Page Design
#* Project Manager/Quality Assurance: Hayden
#* Data Analysis: Mary
#* Coder: Arash
#* Designer: Nicole
# Gene Database APIs
#* Project Manager/Quality Assurance: Corinne
#* Data Analysis: Dina
#* Coders: Eddie A. and John
# JASPAR API
#* Project Manager/Quality Assurance: Quinn
#* Data Analysis: Antonio
#* Coders: Eddie B. and Simon
# Interaction and Integration
#* Project Manager/Quality Assurance: Katie
#* Data Analysis: Emma
#* Coders: Blair and Zach

=== '''Coders and Designer''': Prepare a Journal Club Presentation for Your Assigned Paper ===

Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 14 and Tuesday, November 21. The Coders (and Designer) will present first on November 14, while the QA's and Data Analysts will present second on November 21.

==== Paper Assignments ====
* '''Page Design team:''' Liikkanen, L. A. (2017). The data-driven design era in professional web design. ''interactions'', ''24''(5), 52-57. [https://doi.org/10.1145/3121355 DOI: 10.1145/3121355]
* '''Gene Database APIs team:''' [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting Ford, P. (2015). What is Code? Part 5: The Time You Attended the E-mail Address Validation Meeting. ''Bloomberg Businessweek'' (June 11, 2015).]
* '''JASPAR API team:''' [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made Ford, P. (2015). What is Code? Part 6: How Are Apps Made? ''Bloomberg Businessweek'' (June 11, 2015).]
* '''Interaction and Integration team:''' [https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup-saved-healthcare-gov-the-worst-website-in-america/397784/ Meyer, R. (2015). The secret startup that saved the worst website in America. ''The Atlantic'' (July 9, 2015).]

==== Presentation Prep: Individual Journal Pages ====
In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
# Make a list of at least 10 design or development terms (e.g., techniques, processes, technologies, architectures, environments, etc.) whose definitions you did not know when you first read the article. Define each of the terms. You can use any reputable technology reference source (e.g., [http://developer.mozilla.org Mozilla Developer Network], [https://www.programmableweb.com Programmable Web], etc.) as a source for definitions. If you don’t know where to look, you may look up the term in Wikipedia but ''select a primary or secondary source'' from the Wikipedia article’s references as your actual source. If a technology has an official or definitive website (e.g., https://nodejs.org for Node), cite the '''About''' page within that site for that technology. Cite these definition sources by providing an in-text citation that corresponds to an entry in your References section. Use APA formatting and provide a hyperlink to the URL if it is a web citation. '''''Each definition must have its own citation, even if you used the same overall source.'''''
# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in ''YOUR OWN WORDS'', not copied straight from the article.
#* What is the main message of this work?
#* What is the importance or significance of this work?
#* What design/development practices, processes, techniques, methods, or approaches were described in this work?
#* Briefly state how these activities benefit the endeavors of web design and/or software development.
#* Summarize the main points of the work.
#* What aspects of this work will inform how you carry out your final project?

==== Journal Club Presentation ====

The Coders (and Designer) will prepare and give a 15-minute PowerPoint presentation for their paper in class on Tuesday, November 14.
* Please follow the [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] for how to format your slides.
* You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
* You need to present the information in the outline of your journal article listed above, but organized as a presentation.
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am, Tuesday, November 14.'''''
** You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
* Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the [[Presentation Rubric]].
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
*# What is the speaker's take-home message (one short sentence)?
*# What is the best thing about this presentation?
*# What needs improvement?
*# Please comment on the speaking style (language and delivery) of each presenter.
* Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this one.

=== '''QA's and Data Analysts:''' Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock ===

This exercise will be primarily performed in class on Thursday, November 9. The purpose of this exercise is to create a bibliography of papers that report microarray data from yeast subjected to cold shock. You will present one of the primary research articles you find as a journal club presentation on Tuesday, November 21. You will also use these articles to write the Introduction and Discussion sections of your final group report.

'''Resource:''' [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]

# Create a bibliography of a minimum of 4 citations to primary research articles (2 contributed by the Data Analyst and 2 contributed by the QA) that report microarray data from yeast subjected to cold shock.
#* Each of the 4 references in your bibliography needs to have the following information (an example is given in the section below):
#** The complete bibliographic reference in the APA style (see http://libguides.lmu.edu/content.php?pid=25618&sid=184708. You will be using one of three formats, journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
#** The link to the abstract from PubMed.
#** The link to the full text of the article in PubMedCentral.
#** The link to the full text of the article (HTML format) from the publisher web site.
#** The link to the full PDF version of the article from the publisher web site.
#** Who owns the rights to the article and what is the availability?
#*** Does the journal or the authors own the copyright?
#*** Is the article available “Open Access” upon publication under a Creative Commons license?
#*** If the article is not Open Access, is it available for free after a certain period of time has elapsed?
#** What organization is the publisher of the article?
#*** What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization; see http://oaspa.org/membership/members/ for a list of members of the Open Access Scholarly Publishers Association)
#** Is this article available in print or online only?
#*** Has LMU paid a subscription or other fee for your access to this article?
#** Are the data associated with this article available? If so, provide a link to the dataset.
# You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
#* Use a keyword search for the first three databases/tools and answer the following:
#** PubMed
#*** What original keyword(s) did you use? How many results did you get?
#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** Google Scholar
#*** What original keyword(s) did you use? How many results did you get?
#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#** Web of Science
#*** What original keyword(s) did you use? How many results did you get?
#*** Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
#* Use the advanced search functions for each of these three databases/tools and answer the following:
#** PubMed
#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Google Scholar
#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Web of Science
#*** Which advanced search functions were most useful to narrow down the search? How many results did you get?
#** Perform a prospective search on the following three review articles in Web of Science and answer the following:
#*** Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007). Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews, 31, 327–341. doi: 10.1111/j.1574-6976.2007.00066.x
#**** How many articles does this article cite?
#**** How many articles cite this article?
#*** Al-Fageeh, M.B. & Smales, C.M. (2006). Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal, 397, 247–259. doi: 10.1042/BJ20060166
#**** How many articles does this article cite?
#**** How many articles cite this article?
#*** Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998). Cold shock and adaptation. BioEssays, 20, 49–57. doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N
#**** How many articles does this article cite?
#**** How many articles cite this article?

==== Sample Bibliographic Entry ====

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'', 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
* Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
* Publisher: American Society for Cell Biology (scientific society)
* Availability: in print and online
* Did LMU pay a fee for this article: no

== '''Whole Team Journal Assignment''': Creating a Team Wiki Page ==

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
# Name your team and create your team home page on the wiki.
#* The name of your team home page should simply be the team name.
#* 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.''
# Create a link to your team's page on the course Main page.
# Create a template for your team with useful information and links that you will invoke on all pages that you will create for the project.
#* Create a category using your team name and include it on your team's template so that it also gets used on all pages you will create for the project. Also use include the category "Group Projects" in your template.
#** ''However, please do not add these categories to your own individual templates because we want them to precisely mark pages having to do with the Group Projects and your team, respectively.''
# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

[[Category:Assignment]]
[[Category:Group Projects]]

← Older revision		Revision as of 05:04, 14 November 2017
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−	~~{{Under_Construction}}~~
−
	'''This journal entry is due on Tuesday, November 21, at 12:01 PST.''' ''(Monday night/Tuesday morning)''		'''This journal entry is due on Tuesday, November 21, at 12:01 PST.''' ''(Monday night/Tuesday morning)''

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 * Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this one.
-=== '''Coders and Designer:'''  Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock ===
+=== '''Coders and Designer:'''  Complete Milestones 0 through 3 and begin Milestone 4 ===
 * Coders (and Designer) will complete Milestones 0 through 3 and begin Milestone 4 as detailed on the [[Coder]] page.

← Older revision		Revision as of 00:47, 14 November 2017
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	=== '''Coders and Designer:''' Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock ===		=== '''Coders and Designer:''' Annotated Bibliography of Papers that Report Microarray Data from Yeast Subjected to Cold Shock ===
		+
		+	* Coders (and Designer) will complete Milestones 0 through 3 and begin Milestone 4 as detailed on the [[Coder]] page.
		+	* Individually, each person will keep an electronic lab notebook on his or her individual wiki page detailing the progress made on these milestones for this week.

	== '''Whole Team Journal Assignment''': Creating a Team Wiki Page ==		== '''Whole Team Journal Assignment''': Creating a Team Wiki Page ==

@@ Line 59: / Line 59: @@
 ==== Presentation Prep: Individual Journal Pages ====
 In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
-# Make a list of at least 10 terms for which you did not know the definitions when you first read the article.  Define each of the terms.  You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries.  Cite your sources for the definitions by providing an in text citation that corresponds to an entry in you References section.  Use APA formatting and provide a hyperlink to the URL if it is a web citation.  '''''Each definition must have its own citation, even if you used the same overall source.'''''
+# Make a list of at least 10 terms for which you did not know the definitions when you first read the article.  Define each of the terms.  You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (also see the [http://libguides.lmu.edu/c.php?g=324213&p=2171629#s-lg-box-6606008 BIOL 367 LibGuide] for e-book dictionaries).  Cite your sources for the definitions by providing an in text citation that corresponds to an entry in you References section.  Use APA formatting and provide a hyperlink to the URL if it is a web citation.  '''''Each definition must have its own citation, even if you used the same overall source.'''''
 # Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in ''YOUR OWN WORDS'', not copied straight from the article.
 #* What is the importance or significance of this work?

@@ Line 90: / Line 90: @@
 * Individually, each person will keep an electronic lab notebook on his or her individual wiki page detailing the progress made on these milestones for this week.
-== '''Whole Team Journal Assignment''':  Creating a Team Wiki Page ==
+== '''Whole Team Journal Assignment''':  Revising Your Team Wiki Page ==
-From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments".  For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
+# Make the requested revisions to your team's page.  Feedback will be posted by Thursday, November 16.
 # Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
 # Each team member should reflect on the team's progress:
@@ Line 105: / Line 98: @@
 ## What didn't work?
 ## What will I do next to fix what didn't work?
-# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.
+# Add a citation for each paper presented for journal club by the Coder/Designer and QA/Data Analyst.  Make sure that there are links to the respective PowerPoint presentations as well.
 [[Category:Assignment]]
 [[Category:Group Projects]]

@@ Line 51: / Line 51: @@
 #* Coders: Blair and Zach
-=== '''Coders and Designer''': Prepare a Journal Club Presentation for Your Assigned Paper ===
+=== '''Data Analyst and Quality Assurance''': Prepare a Journal Club Presentation for Your Assigned Paper ===
-Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 14 and Tuesday, November 21.  The Coders (and Designer) will present first on November 14, while the QA's and Data Analysts will present second on November 21.
+The QA's and Data Analysts will give their journal club presentations in class on Tuesday, November 21.
 ==== Paper Assignments ====
-* '''Page Design team:''' Liikkanen, L. A. (2017). The data-driven design era in professional web design. ''interactions'', ''24''(5), 52-57. [https://doi.org/10.1145/3121355 DOI: 10.1145/3121355]
-* '''Gene Database APIs team:''' [https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#the-time-you-attended-the-e-mail-address-validation-meeting Ford, P. (2015). What is Code? Part 5: The Time You Attended the E-mail Address Validation Meeting. ''Bloomberg Businessweek'' (June 11, 2015).]
+''TBA''
 ==== Presentation Prep: Individual Journal Pages ====
@@ Line 65: / Line 63: @@
 # Make a list of at least 10 design or development terms (e.g., techniques, processes, technologies, architectures, environments, etc.) whose definitions you did not know when you first read the article. Define each of the terms. You can use any reputable technology reference source (e.g., [http://developer.mozilla.org Mozilla Developer Network], [https://www.programmableweb.com Programmable Web], etc.) as a source for definitions. If you don’t know where to look, you may look up the term in Wikipedia but ''select a primary or secondary source'' from the Wikipedia article’s references as your actual source. If a technology has an official or definitive website (e.g., https://nodejs.org for Node), cite the '''About''' page within that site for that technology. Cite these definition sources by providing an in-text citation that corresponds to an entry in your References section. Use APA formatting and provide a hyperlink to the URL if it is a web citation. '''''Each definition must have its own citation, even if you used the same overall source.'''''
 # Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser at 100% scale to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in ''YOUR OWN WORDS'', not copied straight from the article.
 #* What is the importance or significance of this work?
-#* What design/development practices, processes, techniques, methods, or approaches were described in this work?
+#* Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
-#* Briefly state how these activities benefit the endeavors of web design and/or software development.
+#* Construct a flow chart that illustrates the above.
-#* Summarize the main points of the work.
+#* Briefly state the result shown in each of the figures and tables.
-#* What aspects of this work will inform how you carry out your final project?
+#* How do the results of this study compare to the results of previous studies (See Discussion).
 ==== Journal Club Presentation ====