BIOL368/F14:Week 4

This journal entry is due on Wednesday, September 24, at midnight PDT. (Tuesday night/Wednesday morning). Note that the OpenWetWare server registers time in the Eastern time zone, so it will say 03:00 AM at midnight PDT.

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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: 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:

• Record your methods, results, and interpretations for the In-class Activity using the Exploring HIV Evolution handout on your individual journal page (an electronic copy of this handout is available on the MyLMU Connect site).
  • Activity 1/Part 2 starting on page 139
  • Activity 1/Part 3
  • Activity 2/Part 1
  • Activity 2/Part 2 ending on page 145
  • Answer the questions throughout the handout on your individual journal page, recording your methods and any files, data, and screenshots that you use to complete the exercise..
• Complete the preparation for the Week 4 Journal Club on your individual journal page. In short, you need to:
  • Prepare your list of 10 vocabulary words and definitions
  • Outline the article.
  • Prepare what you are going to say for your assigned figure/table during the presentation in class.

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

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:

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 (shown in Week 5). Although the project is not due until the Week 5 journal assignment, 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).

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 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/F11" 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?