BIOL368/F20:Week 11

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Fall 2020

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This journal entry is due on Thursday, November 19, at 12:01 PM Pacific time.


Overview

The learning objectives for this assignment are:

  • To evaluate resources for reliability, validity, accuracy, authority, and bias.
  • To explore deeply and critically review an article from the primary scientific literature that will be the basis of our final research project.

Individual Journal Assignment

Homework Partners

  • You will be expected to consult with your partners, 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 the remainder of the semester are:
    • Aiden, Anna, Nida, Taylor
    • Fatimah, JT, Macie, Yaniv
    • Ian, Kam, Nathan, Owen

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. Your template should contain:
    • A link to your user page.
    • A link to the template page itself.
    • A list or table of all of the Assignment pages for the course.
    • A list or table of all of your individual journal pages for the course.
    • A list or table of all the shared class journal pages for the course.
    • The category "BIOL368/F20".
  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 answers to the literature searching exercise and 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 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.

Searching the Scientific Literature Part 2: Evaluating Scientific Sources

  1. Now we will begin to evaluate your assigned article in three areas availability, the journal, and the article metadata. Again, provide a citation for the article in APA format, this time including the DOI. For the following questions, for information that is not available, answer n/a).
    1. Provide a link to the abstract of the article on PubMed
    2. Provide a link to the full text of the article in PubMed Central
    3. Provide a link to the full text of the article (HTML format) from the publisher website.
    4. Provide a link to the full PDF version of the article from the publisher website.
    5. Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
    6. How is the article available to you:
      • Is the article available “open access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
      • If the article is not “open access” is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
      • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
      • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
    7. Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
  2. Evaluating the source--the journal
    1. Who is the publisher of the journal?
    2. Is the publisher for-profit or non-profit?
    3. Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
    4. Does the publisher belong to the Open Access Publishers Association?
    5. What country is the journal published in?
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
    7. Are articles in this journal peer-reviewed?
    8. Provide a link to the scientific advisory board/editorial board of the journal.
    9. What is the journal impact factor (look to see if it is provided on the journal home page; often you can also find it through a Google search)?
  3. Evaluating the source--the article
    1. Is the article a review or primary research article?
    2. On what date was the article submitted?
    3. On what date was the article accepted?
    4. Did the article undergo any revisions before acceptance?
    5. When was the article published?
    6. What is the approximate elapsed time between submission and publication?
    7. What are the institutions with which the authors are affiliated?
    8. Have the authors published other articles on this subject? (How will you find this out?)
    9. Is there a conflict of interest for any of the authors?
    10. Make a recommendation--based just on the information you have gathered so far, is this a good article to evaluate further? Why or why not?
  4. For your Conclusion section of this individual assignment, write a short reflection about what you learned by doing this exercise. Include in your answer what you knew previously about searching the biological literature and evaluating sources, and what you learned that was new that you learned today.

Preparation for Journal Club 2

The paper you are assigned for Journal Club 2:

  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 that you have been assigned in your group.
    • 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 and provide a link to Box in your wiki). Each member of your group should have a link to the same exact 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.
      • Use the Presentation Guidelines PowerPoint on Brightspace when preparing your PowerPoint slides.
      • Your presentation will also be graded on the following Presentation Rubric.

Note: The individual journal entry for this week is worth 10 points like all other journal entries. The journal club presentation is worth 45 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/F20" to the end of the wiki page (if someone has not already done so).

Reflect

  1. What are you wondering about regarding the journal club article that might become the basis for your final research project?
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