BIOL368/F14:Week 5

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 1 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

Background for HIV Evolution Project

References

  1. Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568
  2. Vlahov, D., Anthony, J.C., Munoz, A., Margolick, J., Nelson, K.E., Celentano, D.D., Solomon, L., Polk, B.F. (1991). The ALIVE study, a longitudinal study of HIV-1 infection in intravenous drug users: description of methods and characteristics of participants. NIDA Res Monogr 109, 75-100.

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: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new 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/F14" category to the end of your wiki page.

Electronic Lab Notebook

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

  1. You will answer your research question from Week 4 using the bioinformatics tools you practiced with during the in-class activity.
    • 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. Using your annotated bibliography from Week 3 to interpret your results in light of the data in the more recent papers you found.
  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 interpretation of your results in light of the new papers 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 always, 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).

Note that your journal entry for this week is worth 10 points, like all other journal entry assignments. The research presentation is worth 60 points.


Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14: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/F14" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer these questions on the shared page:

  1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  2. What is still not clear to you after having concluded this project?
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
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