Week 11

This journal entry is due on Tuesday, November 12, at midnight PST. (Monday night/Tuesday morning) Note different due date.

A note on the grading for this assignment:

• The individual journal entry containing the vocabulary definitions and article outline is worth a total of 10 points. Students will be graded on an individual basis for this portion of the assignment.
• The presentation is worth a total of 30 points; each member of the group will receive the same grade for this portion of the assignment.

Individual Journal Assignment

• Store this journal entry as "username Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.

Preparation for Journal Club on Your Species

The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings is another). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research.

In preparation for the Journal Club on Tuesday, November 12, you will each individually complete the following assignment on your individual journal page.

1. Make a list of at least 10 biological 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 the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.
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 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 (i.e., your species)?
   • What were the methods used in the study?
   • 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).
   • In addition to the journal article, please find and review the Model Organism Database (MOD) for your species. In particular, make sure to answer the following:
     1. What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
     2. What individual or organization maintains the database?
     3. What is their funding source(s)?
     4. Is there a license agreement or any restrictions on access to the database?
     5. How often is the database updated?
     6. Are there links to other databases?
     7. Can the information be downloaded?
        • In what file formats?
     8. Evaluate the “user-friendliness” of the database.
        • Is the Web site well-organized?
        • Does it have a help section or tutorial?
        • Run a sample query. Do the results make sense?
     9. What is the format (regular expression) of the main type of gene ID for this species? (for example, for Vibrio cholerae it was VC#### or VC_####).

Team Journal Club Presentation

Each group will prepare and give a 15 minute PowerPoint presentation for their species in class on Tuesday, November 12.

• 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.
  • Specifically, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
• Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, November 12.
  • 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 guidelines shown here.
• 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 are the best points about the presentation's content, organization, clarity of visuals, and presentation style? Please give at least 2 specific examples.
  3. What points need improvement? How would you improve them? Please give at least 2 specific examples.
• 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 presentation.

Team Journal Assignment

Team Wiki Pages

• Please make the requested changes to your team's wiki pages.
  • The genome paper and the DNA microarray paper need to have the following information:
    • Full bibliographic reference according to Guidelines for Literature Citations in a Scientific Paper
    • Link to the HTML version of the full text on the publisher's web site.
    • Link to the PDF version (either uploaded to this wiki if no copyright restrictions or a link to the publisher download site).
  • Please "comment out" the microarray papers that you won't be using for the project.
• Add additional navigation links to your team's pages using a template for your team.
  • Links to individual user pages for the team members.
  • Links to the Gene Database Project main page and Gene Database Project Report Guidelines page.
  • Links to the guild pages.
  • Links to any subpages your team creates.
  • Add the category "Group Projects" in addition to your individual team category.
• Be sure to name your team something other than your species name.