BIOL368/F16:Week 6

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Tuesday, October 11 at midnight PDT (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.


The purpose of this assignment is:

  • To use bioinformatics tools to answer your own questions about the evolution of the HIV virus using the Markham et al. (1998) dataset.
  • To communicate the results of your research in a scientific presentation with a clear and consistent message.

Background for HIV Evolution Project


  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 6" (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/F16" category to the end of your wiki page.

Homework Partners

Your partners for the HIV Evolution Project are the same as last week and for the remainder of this project. Please sit next to your partner in class.

  • Matthew Allegretti, Isai Lopez
  • Shivum Desai, Zachary Goldstein
  • Jordan Detamore, Matthew Oki
  • William Fuchs, Colin Wikholm
  • Mia Huddleston, Anu Varshneya
  • Courtney Merriam, Avery Vernon-Moore

HIV Evolution Project and 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:

Your notebook entry should contain the progress you have made on your project, including:

  • The purpose: what was the purpose of your investigations?
  • Record your methods and results of what you have done so far on the research 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).
  • References to data and files should be made within the methods/results section of your notebook.
  • In addition to these inline links, create a Data and Files section of your notebook to make a list of the files generated in this exercise.
    • Remember to back up your files in at least two ways.
  • A scientific conclusion: what was your main finding for today's work; briefly summarize the progress you made towards your research question?

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

Scope of the Research Project for Weeks 5 and 6

  1. You will answer your research question from Week 4 using the bioinformatics tools with which you practiced during the in-class activities for Weeks 3 and 4.
    • 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 annotated bibliography from this week to interpret your results in light of the data in the more recent papers you found.
  3. You will prepare a presentation that you will give in class for Week 7 (October 11) 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 (you will need to provide some summary of the Markham et al. 1998 article for this)
      • 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 6 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.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.


In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
      • Sign this statement with your wiki signature.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
  4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."


  • In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • data
    • facts
    • images
    • documents, including the scientific literature
  • The references in this section should be accompanied by in text citations on your page that refer to these references.
  • The references should be formatted according to the APA guidelines.
  • For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F16:Class Journal Week 6 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/F16" category to the end of the wiki page (if someone has not already done so).


  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?