BIOL368/S20:Week 14

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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This journal entry is due on Thursday, April 30, at 12:01am Pacific time.


Overview

The learning objectives for this assignment are:

Individual Journal Assignment

Homework Partners

  • You will be expected to consult with your partners, in order to complete this assignment and the final project and presentation.
  • 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 are:
    • Annika, Christina, Sahil
    • Carolyn, Jenny, Nathan
    • Drew, Jack, Nick
    • Karina, Madeleine, Maya, Lizzy

Format and Content Checklist

  1. Store this journal entry as "username Week 14" (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.
  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 this exercise. 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.
    • Answers to any specific questions posed in the exercise.
    • 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 in this exercise.
  6. Scientific Conclusion: a summary statement of the main result of exercise/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.

General Tools

Data Collections

Data

Scope of the Coronavirus Structure Research Project

  1. You will answer your research question from Week 13 using the bioinformatics tools with which you practiced during the in-class activities for Weeks 13. Dr. Dahlquist will approve all project questions and provide assistance with finding data.
    • You must create a multiple sequence alignment and tree using Phylogeny.fr (or other equivalent software).
    • You must create one or more structure visualization figures to illustrate your results.
  2. You will prepare a presentation that you will give in class for Week 14 (April 29) 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 can use some background from your journal club 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 14 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 14 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

For your last reflection you will reflect on this entire semester:

  • What is the most important thing that you learned this semester in this class?
    • With your head (biological or bioinformatics principles)?
    • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • With your hands (technical skills)?
  • What will you take away from this class that you will still use a year from now?
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