# BIOL368/F16:Week 5

BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

This journal entry is due on Tuesday, October 4 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.

## Grading for This Week's Assignment

The Annotated Bibliography that you will complete for this week's assignment is one of two Information Literacy assignments this semester.

• This week's assignment is worth a total of 30 points--10 + an additional 20 points because it is an information literacy assignment.
• The shared journal is worth 3 points, as usual.

## Overview

The purpose of this assignment is:

• To select information that provides relevant evidence for a topic.
• Find and use scholarly and discipline-specific professional information, including major literature databases for the biomedical research community.
• To differentiate between source types (primary research article vs. review; publishers and access).
• To use bioinformatics tools to answer your own questions about the evolution of the HIV virus using the Markham et al. (1998) dataset.

## Background for HIV Evolution Project

### 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
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 5" (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.)
• Don't forget to add the "BIOL368/F16" category to the end of your wiki page.

### Homework Partners

Your partners for the HIV Evolution Project are the same as last week and for the remainder of this project. Please sit next to your partner in class.

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

### Annotated Bibliography for HIV Evolution Project

Note that this assignment was handed out as a paper copy in class because the OWW wiki was down. Every effort has been made to make this wiki assignment match the one handed out, but in case of discrepancy, follow the one given to you in class which is linked here.

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:

• Throughout today's exercise, bear in mind the research questions developed by you and your partner as part of the Week 4 assignment.
• The Markham et al. article was published in 1998, 18 years ago. You will use the bibliographic databases and tools introduced in today's guest lecture to:
1. Create a bibliography of a minimum of 3 citations to primary research articles and 1 review article, for a total of 4 articles that are related to the Markham et al. (1998) article and include information about the evolution of the env gene. Each partner in a group must find 4 different articles from each other. Thus, this assignment should be completed individually, consulting each other for assistance and to make sure that you are finding different articles.
• The articles need to have been published in the last five years (publication date of 2012-2016).
• Each of the 4 references in your bibliography needs to have the following information (an example is given at the end of the assignment handout):
• The complete bibliographic reference in the APA style (see 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, if applicable.
• The link to the full text of the article (HTML format) from the publisher web site.
• Who owns the rights to the article and what is the availability?
• Does the journal or the authors own the copyright?
• Is it available “Open Access” upon publication under an alternative license such as Creative Commons?
• Is the article available for free after a certain period of time has elapsed?
• Is the article only available behind a paywall (use ILLiad for access)?
• What organization is the publisher of the article?
2. You must use these three databases/tools to find the references that you include in your bibliography, using both the basic and advance search functions.:
• PubMed
• 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?
• Which advanced search functions were most useful to narrow down the search? How many results did you get?
• 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?
• Which advanced search functions were most useful to narrow down the search? How many results did you get?
• Web of Science
• 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?
• 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?

Optional:

• You may choose to create your bibliography using the free citation management software, Zotaro. (See http://libguides.lmu.edu/content.php?pid=442493&sid=3623452)
• 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.

#### Appendix: How to find the information to answer the questions about each bibliographic entry:

• The “shortcut” way to get an APA-formatted citation that you can copy and paste into your wiki is to look up the citation in Google Scholar, and then click on the “cite” link under the article in the search results. This will open a pop-up window showing the properly formatted bibliographic citation that you can copy and paste. However, there are two caveats to doing this:
• This citation does not automatically provide the DOI number, so you will need to add that to your citation, if it is available. The DOI number can be found on the PubMed abstract page, the publisher full text page, or on the PDF of the article iteslf.
• You will still need to use wiki syntax to add italics in the proper place in the citation.
• Click on the link for an individual article in your PubMed search results to get to the PubMed abstract page. Some articles do not have abstracts (although this is rare).
• PubMed Central is a repository for the full text of articles that have been published as a result of NIH funding. Sometimes these articles look identical to the publisher form of the article, and sometimes they are formatted differently. You can find a link to the PubMed Central version of the article (if it exists) from the PubMed abstract page (upper right corner). You should always use the publisher form of the article, if it is available.
• The link to the full text of the article on the publisher web site is usually found on the PubMed abstract page or as the main link of the Google Scholar result. Sometimes you need to go to the publisher site first to find the article (although this is rare). “HTML” refers to the article formatted for easy viewing on a web site.
• If you want to print an article, do not print from the web site because you will waste a lot of paper; instead print out the PDF version.
• However, when you are copying figures for a PowerPoint presentation, it is best to copy them from the web site version.
• The link to download the PDF version of the article is found somewhere on the page of the full text of the article on the publisher web site.
• The copyright notice should be on the first page of the PDF version of the article. If the article is open access, there is usually an icon of a padlock in the unlocked position and information about the license. If you are accessing the article for free and it doesn’t say “open access” then it is probably from a journal that releases articles after some time has passed after publication.
• The publisher is the corporation that publishes the journal; usually a single large publisher publishes many journals. The publisher information is found on the web site of the journal. Some common ones are:
• For profit: Nature Publishing Group, Springer, Elseveir
• Scientific Societies: American Association for the Advancement of Science (publishes Science), American Society for Cell Biology (publishes Molecular Biology of the Cell), American Society for Biochemistry and Molecular Biology (publishes Journal of Biological Chemistry).
• Respected Open Access publishers: Public Library of Science (PLoS), BioMed Central
• Print availability: on the publisher web site, click on a link to “subscriptions” which will tell you if it is available in print. Many newer open access journals are online-only, while many older, well-established journals are available both in print and online.
• To find out whether LMU paid a fee for the article, you need to look to see if it is listed in the LMU list of journals, found here: http://sq4ya5rf2q.search.serialssolutions.com/
• 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

### HIV Evolution Project and Electronic Lab Notebook

Complete your electronic notebook for this week's part of the HIV Evolution project on your individual journal page. Your notebook entry should contain:

• The purpose: what was the purpose of your investigations?
• Record your methods and results of what you have done so far on the research 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).
• 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; briefly summarize the progress you made towards your research question?

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

#### Scope of the Research Project for Weeks 5 and 6

1. You will answer your research question from Week 4 using the bioinformatics tools with which you practiced during the in-class activities for Weeks 3 and 4.
• You must create a multiple sequence alignment and tree using ClustalW.
• You must also use one of the statistics you calculated, S, θ, or the Min and Max distances (or some other statistic mentioned in the Markham et al. (1998) paper.
2. Use your annotated bibliography from this week to interpret your results in light of the data in the more recent papers you found.
3. For your Week 5 individual journal assignment, you and your partner should make an outline of what methods/procedures/steps that you will use to analyze your data and answer your research question so that you are ready to work on it in class on October 4 (Week 6).
4. You will prepare a presentation that you will give in class for Week 7 (October 11) showing your results.
• Your presentation 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 (you will need to provide some summary of the Markham et al. 1998 article for this)
• Discussion and interpretation of your results in light of the new papers you found.

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.
• 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 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).