BIOL368/F16:Week 3

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Tuesday, September 20 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 week's assignment is to:

  1. Deeply explore and critically review an article from the primary scientific literature that will be the basis of our first research project.
  2. Learn how to work with DNA sequence data and the Biology Workbench.

Background for HIV Evolution Project


  1. Donovan S and Weisstein AE (2003) Exploring HIV Evolution: An Opportunity for Research. In Jungck JR, Fass MR, and Stanley ED, eds. Microbes Count! West Chester, Pennsylvania: Keystone Digital Press.
  2. 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
  3. 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 3" (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 Preparation for Week 4 Journal Club exercise below on your individual journal entry page.

Homework Partners

You will work in groups of two for this week's assignment. Please sit next to your partner in class. You will be expected to consult with your partner, in order to complete the assignment. 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). Homework partners for this week are:

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

Exploring HIV Evolution In-Class Activity & Electronic Lab Notebook

Complete your electronic notebook for the assigned parts of the Exploring HIV Evolution 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 1/Part 2 starting on page 139
    • Activity 1/Part 3 ending on page 141
  • 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?

Preparation for Week 4 Journal Club

"Science... is a process taking place in the minds of living scientists," (Curtis, 1983). The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings are others). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research. This is the first of three journal club discussions we will have this semester. For this first journal club, the entire class will read and present the Markham et al. (1998) paper referenced above. Each student will create an individual wiki journal page for their Week 3 assignment and also contribute to the shared journal page in preparation for the presentation in class on September 20.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.
  2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • How did they overcome these limitations?
    • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
    • How do the results of this study support published HIV evolution models?
    • What are the limitations in this study? (your critical evaluation of the study).
    • What future work do you suggest?
  3. Each pair of students will be assigned a table and/or figure. You will be responsible for explaining the table/figure in detail to the class, including the methods used to obtain that figure/table. The instructor will provide the PowerPoint presentation slides containing the figures and tables you will present.
    • Figure 1: Matt Allegretti, Will Fuchs
    • First five data columns of Table 1: Shivum Desai, Jordan Detamore
    • Last three data columns of Table 1: Zachary Goldstein, Isai Lopez
    • Figure 2A: Mia Huddleston, Courtney Merriam
    • Figure 2B: Matt Oki, Colin Wikholm
    • Figures 3 & 4: Anu Varshneya, Avery Vernon-Moore

Online Biological Dictionaries

How to Read a Primary Research Article

A primary research article is divided into sections that each have a different purpose. Articles in Science and Nature are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.


The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on PubMed and may be the only part of the text publicly available.


The introduction gives the background information necessary to understand the paper. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

  • States importance of the problem
  • States what is known about the problem
  • States what is unknown about the problem
  • States clues that suggest how to approach the unknown
  • States the question the paper is trying to address
  • States the experimental approach
  • Sometimes briefly states the answer they found

Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.


Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.


States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.


List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

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 3 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).


Answer these questions on the shared page:

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
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