BIOL368/F11:Week 7

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 19 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.


Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL368/F11" category to the end of your wiki page.

Preparation for Week 8 Journal Club

The class will be divided into groups of 3 or 4. Each group will create and present a Journal Club (in class in Week 8) on the Kwong et al. (1998), Stanfield et al. (1999), or Stanfield et al. (2003) articles. The groups will be:

  • Kwong et al. (1998): Nicki, Sam, and Zeb
  • Stanfield et al. (1999): Alex, Chris
  • Stanfield et al. (2003): Robert, Isaiah

In preparation for the Journal Club, each individual will do the following assignment on their individual Week 7 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 (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page, along with the date accessed is fine.
  2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (use the "Print Preview" menu item in your browser to check your 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 result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • 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 (Include an outline of the Discussion).
  3. This time your group will prepare the PowerPoint slides for your Journal Club Presentation.
    • Include the following slides:
      • Title slide with the full citation of the journal article: authors, year, title, journal name, volume, page numbers, the names of the group members, the date, and the class number and title.
      • Outline slide
      • Introduction slide(s) to HIV
      • A slide for every figure and table in the paper with an explanatory title that is a phrase or sentence that explains the main point of the figure/table.
      • One or more slides based on the Discussion and summarizing the paper (your outline slide can become your summary if reworded properly.
    • Upload your slides to the OpenWetware wiki by the Week 7 journal assignment deadline. Each member of your group should have a link to the same PowerPoint file. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F11:Class Journal Week 7 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F11" category to the end of the wiki page (if someone has not already done so).

Reflection

  1. What was the easiest aspect of reading/understanding the your journal club article?
  2. What was the most difficult aspect of reading/understanding your journal club article?
  3. What new question do you have about HIV that you would like to answer?
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