Week 12

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 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 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:

1. Page Design
   • Project Manager/Quality Assurance: Hayden
   • Data Analysis: Mary
   • Coder: Arash
   • Designer: Nicole
2. Gene Database APIs
   • Project Manager/Quality Assurance: Corinne
   • Data Analysis: Dina
   • Coders: Eddie A. and John
3. JASPAR API
   • Project Manager/Quality Assurance: Quinn
   • Data Analysis: Antonio
   • Coders: Eddie B. and Simon
4. Interaction and Integration
   • Project Manager/Quality Assurance: Katie
   • Data Analysis: Emma
   • Coders: Blair and Zach

Data Analyst and Quality Assurance: Prepare a Journal Club Presentation for Your Assigned Paper

The QA's and Data Analysts will give their journal club presentations in class on Tuesday, November 21.

Paper Assignments

TBA

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.

1. 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 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.
2. 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?
   • Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
   • Construct a flow chart that illustrates the above.
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies (See Discussion).

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 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:
  1. What is the speaker's take-home message (one short sentence)?
  2. What is the best thing about this presentation?
  3. What needs improvement?
  4. 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.

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.
• 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: Revising Your Team Wiki Page

1. Make the requested revisions to your team's page. Feedback will be posted by Thursday, November 16.
2. 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).
3. Each team member should reflect on the team's progress:
   1. What worked?
   2. What didn't work?
   3. What will I do next to fix what didn't work?
4. 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.