BIOL368/S20:Week 6

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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This journal entry is due on Thursday, February 27, at 12:01am Pacific time.


Overview

The learning objectives for this assignment are:

  • To use bioinformatics tools to answer your own questions about the evolution of the HIV virus using the Markham et al. (1998) dataset.
  • To communicate the results of your research in a scientific presentation with a clear and consistent message.

Individual Journal Assignment

Homework Partners

  • You will be expected to consult with your partner, in order to complete the assignment.
  • Each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
  • You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment.
  • Homework partners for this week are:
    • Christina and Annika
    • Jenny and Nick
    • Drew and Jack
    • Karina, Lizzy and Sahil
    • Madeleine and Maya
    • Carolyn and Nathan

Format and Content Checklist

  1. Store this journal entry as "username Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
  2. Write something in the summary field each time you save an edit. You are aiming for 100%.
  3. Invoke the template that you made as part of the Week 1 assignment on your individual page. Your template should contain:
  4. Purpose: a statement of the scientific purpose of the assignment. Note that this is different than the learning objective stated on the assignment page. What science will be discovered by completing this assignment?
  5. Combined Methods/Results (Electronic Lab Notebook): documentation of your workflow for your HIV Evolution Project. It should include:
    • The protocol you followed in enough detail for someone else to be able to conduct the same investigation. There should be enough detail provided so that you or another person could re-do it based solely on your notebook. You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
    • Screenshots and images to document your answers.
    • Data and files: links to all data and files used and generated.
      • Files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the T: drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
      • Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
      • References to data and files should be made within the methods and results section. In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated during your research.
  6. Scientific Conclusion: a summary statement of the main result of research. It should mirror the purpose. Length should be 2-3 sentences, up to a paragraph.
  7. Acknowledgments section (see Week 1 assignment for more details.)
    • You must acknowledge your homework partner with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together.
    • Acknowledge anyone else you worked with who was not your assigned partner. This could be the instructor, the TA, other students in the class, or even other students or faculty outside of the class.
    • 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 copied any part of the assignment or protocol and then modified it, acknowledge that here and also include a formal citation in the Reference section.
    • You must also include this statement:
    • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
    • Sign your Acknowledgments section with your wiki signature (four tildes, ~~~~).
  8. References section (see Week 1 assignment for more details.)
    • Use the APA format.
    • Cite this assignment page.
    • Cite any protocols that you copied and modified (this must also be noted in the Acknowledgments section).
    • Cite any other methods, software, websites, data, facts, images, documents (including the scientific literature) that was used to generate content on your page.
    • Do not include extraneous references that you do not cite or use on your page.

Resources, Links, Data, and Files

Scope of the HIV Evolution Research Project

  1. You will answer your research question from Week 5 using the bioinformatics tools with which you practiced during the in-class activities for Weeks 5.
    • You must create a multiple sequence alignment and tree using Phylogeny.fr (or other equivalent software).
    • You must also use one of the statistics you calculated, S or θ (or some other statistic mentioned in the Markham et al. (1998) paper.
  2. You will prepare a presentation that you will give in class for Week 7 (February 27) 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
      • Future directions
    • Upload your slides to the OpenWetWare wiki by the Week 7 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.

Shared Journal Assignment

  • Compose your journal entry in the shared Class Journal Week 6 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Create a header with your name, and then answer the questions in your own section of the page.
  • You do not need to invoke your template on the class journal page.
  • Any 'Acknowledgments and References you need to make should go in the appropriate sections on your individual journal page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the category "BIOL368/S20" to the end of the wiki page (if someone has not already done so).

Reflect

  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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