BIOL368/F16:Week 5: Difference between revisions

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* William Fuchs, Colin Wikholm
* William Fuchs, Colin Wikholm
* Mia Huddleston, Anu Varshneya
* Mia Huddleston, Anu Varshneya
 
* Courtney Merriam, Avery Vernon-Moore


=== Annotated Bibliography for HIV Evolution Project ===
=== Annotated Bibliography for HIV Evolution Project ===

Revision as of 15:32, 20 September 2016

This page is currently under construction.

BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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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.


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.)
    • 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.

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

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, 18 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

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.


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:

  1. You will answer your research question from Week 4 using the bioinformatics tools you practiced with 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. 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)
      • Your question
      • How you answered your question, method/results
      • Interpretation of your results; answer to your question
      • Discussion and interpretation of your results in light of the new papers you found.
    • Upload your slides to the OpenWetWare wiki by the Week 6 journal assignment deadline. You may make changes to your slides in advance of your presentation, but you will be graded on what you upload by the journal deadline.


Furthermore, as always, 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.
      • 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 :) )
  • 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. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  2. What is still not clear to you after having concluded this project?
  3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
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