BIOL368/F16:Week 4

This journal entry is due on Tuesday, September 27 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.

Overview

The purpose of this week's assignment is to:

• Learn several ways to quantify sequence similarity and difference.
• Ask your own questions and develop your own hypotheses to explain patterns in the Markham et al. (1998) dataset.

Background for HIV Evolution Project

• BEDROCK HIV Problem Space
  • Sequence Data
  • Media:Visit_1_Subjects_1_thru_9_HIV.txt
  • Media:Visit_1_Subjects_10_thru_15_HIV.txt
• HIV Database at Los Alamos National Laboratory
• Biology Workbench
  • Orientation to the Biology Workbench
• Sigma notation calculator

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
   • Publisher Full text
   • PDF.
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.
   • PubMed
   • PDF.

Individual Journal Assignment

• Store this journal entry as "username Week 4" (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/F16" category to the end of your wiki page.
• Complete your electronic notebook for the Exploring HIV Evolution In-Class Activity below.
• Define your research project by answering the questions below.

Homework Partners

You will work in groups of two for this week's assignment and for the remainder of the HIV Evolution Project. Please sit next to your partner in class. You will be expected to consult with your partner, in order to complete the assignment and project. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). I am choosing the partners for this first project so that you learn to work with as many different members of the class as possible; you will have the opportunity to choose your own partners/teams for subsequent projects. Homework partners for this week are:

• Matthew Allegretti, Isai Lopez
• Shivum Desai, Zachary Goldstein
• Jordan Detamore, Matthew Oki
• William Fuchs, Colin Wikholm
• Mia Huddleston, Anu Varshneya

Exploring HIV Evolution In-Class Activity & Electronic Lab Notebook

We will continue with the Exploring HIV Evolution activity we started last week. Complete your electronic notebook for the assigned parts of the exercise on your individual journal page (an electronic copy of this handout is available on the MyLMU Connect site). Your notebook entry should contain:

• The purpose: what was the purpose of your investigations?
• Record your methods and results, answering the questions throughout the handout, for the Activities we will complete this week:
  • Activity 2/Part 1 starting on page 141
  • Activity 2/Part 2 ending on page 145
• 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 exercise? Did you fulfill the purpose? Why or why not?

Defining Your Research Project

For this portion of your journal assignment, your electronic lab notebook entry should contain the answers to the questions below, which will define your HIV Evolution research project for the next couple of weeks. For this portion of the assignment only, both partners may have the same text on their individual journal pages (since you will develop the answers together for your joint project).

1. What is your question?
2. Make a prediction (hypothesis) about the answer to your question before you begin your analysis.
3. Which subjects, visits, and clones will you use to answer your question?
   • You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
   • Justify why you chose the subjects, visits, and clones you did.

Once you have your question, hypothesis, and data you will use, you should then move on to answering your question (see the Week 5 Assignment). Although the project is not due until October 11, you should work ahead. 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).

Academic Honesty

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

Acknowledgments

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. We agreed upon our research question for the HIV Evolution project.
     • 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."

References

• 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 4 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/F16" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer these questions on the shared page:

1. Did the in-class discussion of the journal article enhance your understanding of the article? Why or why not?
2. Have your views about what it means to do original research in biology changed as a result of discussing this article? Why or why not?
3. What are the characteristics that you look for in a team member for a successful group project?