BIOL368/F14:Week 3

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, September 17 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

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 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/F14" category to the end of your wiki page.
  • Complete both the Annotated Bibliography for HIV Evolution Project and Preparation for Week 4 Journal Club exercises below on your individual journal entry page.

Annotated Bibliography for HIV Evolution Project

The reference librarian for the sciences, Glenn Johnson-Grau will be giving a guest lecture today to prepare you for this exercise.

Bioinformatics servers and online biological databases are a moving target. They change frequently, and manuals go out of date quickly. Today we will explore online literature databases because the first step in any research project is to find out what is previously known about the subject in the published literature. Your goal is to find out published information about the HIV virus that will help you understand the HIV evolution project. You will also use these articles to interpret and discuss your results of the project. To begin:

  • Write three questions (or more) that you have about HIV that you would like answered.
  • The Markham et al. article that you will read and present next week for your first journal club was published in 1998, 16 years ago. You will use the bibliographic databases and tools introduced in today's guest lecture to create an annotated bibliography of a minimum of 3 citations to recent primary research articles and 1 citation to a recent review article that are related to the Markham et al. (1998) paper and include information about the evolution of the env gene.
    • The articles need to have been published in the last five years.
    • You must use these three databases/tools to find the references that you include in your bibliography:
    • Using a keyword search answer the following:
      • What original keyword(s) did you use? How many results did you get?
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • Use the advanced search functions for each of these three databases/tools and answer the following:
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
    • Perform a prospective search on the Markham et al. (1998) article and answer the following:
      • How many articles does the Markham et al. (1998) article cite?
      • How many articles cite the Markham et al. (1998) article?
    • Create a bibliography on your Week 3 journal page that has the following information:
      • The complete bibliographic reference in the APA style (see the Citation Styles LibGuide or the Writing LibGuide). You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
      • The link to the abstract from PubMed.
      • The link to the full text of the article in PubMedCentral.
      • The link to the full text of the article (HTML format) from the publisher web site.
      • The link to the full PDF version of the article from the publisher web site.
      • Who owns the copyright of the article? Is it available “Open Access” under an alternative license such as Creative Commons?
      • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization) (Open Access Scholarly Publishers Association Members)
      • Is this article available in print or online only?
      • For example, see the bibliographic entry for Markham et al. (1998) below which is available both in print and online:

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


  • You may choose to create your bibliography using the free citation management software, Zotaro. (See
  • Zotaro will allow you to save a list of references and then output them in the APA form requested in the assignment. You will still need to answer the additional questions for each reference. If you choose this option, export your bibliography into rich text format (.rtf), upload it to OpenWetWare, and link to the file from your individual journal page.

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 17.

  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 main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • 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).
  3. Each student 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 & first five data columns of Table 1: Nicole
    • Figure 2 & last three data columns of Table 1: Chloe
    • Figures 3 & 4: Isabel

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.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14: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/F14" 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 online bibliographic databases and 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?