BIOL368/F11:Week 5

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 5 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.

Individual Journal Assignment

  • Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
    • 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.

Electronic Lab Notebook

Complete your electronic notebook for this week's part of the BIOL368/F11:HIV Evolution project on your individual journal page. Your notebook entry should contain:

  • The information requested as part of the Literature Search Activity.
  • The continuation of your HIV Evolution Research Project. Specifically:
    1. You will then answer your research question from Week 4 using the bioinformatics tools you practiced with in Week 3.
      • You must create a multiple sequence alignment and tree using ClustalW.
      • You must also use one of the statistics you calculated, S, θ, or the Min and Max distances (or some other statistic mentioned in the Markham et al. (1998) paper.
    2. Use your Web of Science prospective literature search results from the in-class activity to select a paper that was published within the last 5 years that studies the evolution of the env gene, in particular the V3 region, if possible. Include the bibilographic reference to this paper in your Week 5 journal.
      • Interpret your results in light of the data in this new paper.
    3. You will prepare a presentation for Week 6 showing your results.
      • Your presentation will be 15 minutes long (approximately 15 slides, one per minute). Include:
        • Title slide
        • Outline slide
        • Background that led you to ask your research question (summary of Markham et al. 1998)
        • Your question
        • How you answered your question, method/results
        • Interpretation of your results; answer to your question
        • Discussion and interprettion of your results in light of the new paper you found.
      • Upload your slides to the OpenWetware wiki by the Week 5 journal assignment deadline. 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.

Furthermore, as alwasy, your electronic notebook should contain your notes, methods, results, and interpretations as you carry out your project. You should document as you work, taking your notes on the wiki as much as possible. Post data, figures, screenshots, to support your project. You can post files that are in progress; remember, you can upload a new version of the file and the wiki will automatically link to the new version (while keeping the old).

Although you will have assigned partner(s), you will need to fill out your own individual journal page with your own work.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F11:Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to the shared journal entry from your user page.
  • 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).


Answer these questions on the shared page:

  1. What was the best part of working with a partner on this project? What was the worst part?
  2. Besides the scientific conclusion of your project, what have you learned about the process of doing research as a result of this project?