BIOL368/F16:Week 11

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Tuesday, November 15 at midnight PST (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

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).
  • 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

Please sit next to your partner in class.

  • Zach, Jordan
  • Colin, Isai
  • Anu, Matt A.
  • Matt O., Will
  • Mia, Avery
  • Shivum, Courtney

Electronic Notebook

Your notebook entry should contain the documentation for you HIV Structure Research Project. Note that an electronic notebook entry should include the following elements:

  • The purpose: what was the purpose of your investigations?
  • Record your methods and results of what you did. You should document as you work, taking your notes on the wiki as much as possible. Post data, figures, and screenshots. 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?

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

HIV Structure Project

For this week, you will complete the investigation of the structure of the gp120 protein and answer your research question and finalize your slides for your research presentation to be given in class next week.

  1. Your presentation for Week 12 will be formatted similarly to the previous HIV Evolution Project. In this case, you will want to work on creating structure figures that illustrate what result you are trying to show.
    • Your formal presentation for Week 12 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
      • Your question
      • How you answered your question, method/results
      • Interpretation of your results; answer to your question
    • Upload your slides to the OpenWetWare wiki by the Week 12 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 11 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).

Read & Reflect

For this week's reflection, we will connect with the human face of AIDS by reading selections from Global AIDS: Myths & Facts by Alexander Irwin, Joyce Millen, and Dorothy Fallows, posted on MyLMU Connect.

We will assign chapters ("myths") from this book in class. You will read your assigned chapter, write a short summary on the shared journal page, and be prepared to discuss your section with the class next Tuesday after the presentations.

  • Matt A.: Preface, Introduction, HIV/AIDS Basics
  • Shivum D.: Myth One: AIDS and Africa
  • Jordan D.: Myth Two: Dangerous Behavior
  • Will F.: Myth Three: Corruption
  • Zach G.: Myth Four: Prevention vs. Treatment?
  • Mia H.: Myth Five: Obstacles to AIDS Treatment
  • Isai L.: Myth Six: Vaccines
  • Courtney M.: Myth Seven: Profits vs. Health
  • Matt O.: Myth Eight: Limited Resources
  • Anu V.: Myth Nine: Nothing to Gain
  • Avery V.-M.: Myth Ten: Nothing We Can Do
  • Colin W.: Conclusion, Resources for Activism