BIOL368/S20:Week 11

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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 16, at 12:01am Pacific time.


The learning objectives for this assignment are:

  • To explore deeply and critically review an article from the primary scientific literature that will be the basis of our final research project.
  • To deliver an effective journal club presentation, improving upon your presentation skills.

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, Drew, Maya: Wan et al. (2020)
    • Annika, Jenny, Sahil: Wrapp et al. (2020)
    • Carolyn, Karina, Jack: Yan et al. (2020)
    • Madeleine, Nathan, Nick: Walls et al. (2020)
    • Lizzy: Wan et al. (2020)

Format and Content Checklist

  1. Store this journal entry as "username Week 11" (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. For this week, your electronic lab notebook will consist of the definitions and article outline described below.
  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 partners 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, 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 the sources for your definitions.
    • Cite the journal club article.
    • Cite any other resources you used for your page.
    • Do not include extraneous references that you do not cite or use on your page.

Preparation for Journal Club 2

Each group has been assigned one of four papers about the structural biology of the SARS-CoV-2 spike protein (see Homework Partners sectiion).

Each student will create an individual wiki journal page for his or her Week 11 assignment and will contribute to the preparation of a group PowerPoint presentation that will be given in class on April 16.

  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 citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page. Note that the citation should be to the exact page from which the definition was taken, not to the general home page of the the online dictionary.
  2. Write an outline of the article. The length should be the equivalent of 2-3 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. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • How did they overcome these limitations?
    • 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 were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
    • How do the results of this study compare to the results of previous studies (See Discussion).
    • What are the important implications of this work?
    • What future directions should the authors take?
    • Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any limitations or major flaws to the paper?
  3. This time your group will prepare the PowerPoint slides for your Journal Club Presentation.
    • Include the following slides:
      • Title slide with the full citation of the journal article in APA format (authors, year, title, journal name, volume, page numbers, DOI) the names of the presenting group members, the date, and the course number and title.
      • Outline slide
      • Introduction slide(s) about SARS-CoV-2
      • A slide for every figure and table in the paper with an explanatory title that is a phrase or sentence that explains the main point of the figure/table.
      • One or more slides based on the Discussion and summarizing the paper (your outline slide can become your summary if reworded properly).
    • Upload your slides to the OpenWetWare wiki by the Week 11 journal assignment deadline (Alternately, you can upload to Box). Each member of your group should have a link to the same file. 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.

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The journal club presentation is worth 50 points. The same presentation grade will be given to the entire group, except for the individual delivery portion of the grade.

Online Biological Dictionaries

Shared Journal Assignment

  • Compose your journal entry in the shared Class Journal Week 11 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).


  1. What was the easiest aspect of reading/understanding the your journal club article?
  2. What was the most difficult aspect of reading/understanding your journal club article?
  3. What new questions do you have about SARS-CoV-2 that you would like to answer in the final project?
    • Note that usually the final project is a structure-function project, but I am open to other ideas for projects as long as they involve a substantial data analysis component.

Partner Requests

  • Partners for the final project will be mostly groups of two and one group of three.
  • Send Dr. Dahlquist an e-mail with your partner requests by 9:00 AM PDT on Thursday, April 16.
  • Tell me the names of three people that you want to work with and one name of a person you do not want to work with. I will try to accommodate everyone in setting up the partners.