BIOL368/F20:Week 10

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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 12, at 12:00 PM Pacific time. Note different time!


Overview

The learning outcomes for this assignment are:

  • Students will be able to select information that provides relevant evidence on a topic.
  • Students will be able to find and use scholarly and discipline-specific professional information, understanding the role of journals and publishers in controlling and providing access to scholarly content.
  • Students will be able to differentiate between primary and secondary sources, recognizing how their use and importance vary with each discipline.

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:
    • Aiden & Ian
    • Anna & Nathan
    • Fatimah & Macie
    • JT & Taylor
    • Kam & Yaniv
    • Nida & Owen

Format and Content Checklist

  1. Store this journal entry as "username Week 10" (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. Answers to the specific questions posed in the exercise. You may copy the questions from the assignment to your individual journal page as long as you acknowledge that you did that in your Acknowledgments section.
  6. Scientific Conclusion: See the assignment below for a description of what needs to go into your Conclusion section.
  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.)
    • For this week, you will only need to cite the Week 9 assignment page and the source database pages, Google Scholar, PubMed, and Web of Science. You do not need to re-list the references you found as part of the assignment.
    • Use the APA format.
    • Do not include extraneous references that you do not cite or use on your page.

Resources

Assignment

The goal for this assignment is to create a class shared annotated bibliography of references for the second SARS-CoV-2 research project.

  1. Warm up exercise (announced in class).
  2. Perform a search in Google Scholar .
    1. Record the number of “hits” you found:
    2. Record the top 10 papers, this time using APA format:
      • paper 1 (remove this placeholder when you are answering this question on your own page).
      • paper 2
      • paper 3
      • paper 4
      • paper 5
      • paper 6
      • paper 7
      • paper 8
      • paper 9
      • paper 10
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • paper 1
    • paper 2
    • paper 3
    • paper 4
    • paper 5
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • paper 1
    • paper 2
    • paper 3
    • paper 4
    • paper 5
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • paper 1
    • paper 2
    • paper 3
    • paper 4
    • paper 5
  6. We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • search terms
    • Record the search terms that have now been assigned specifically to you:
  7. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:
    • Record the top 10 papers (you don't need to do APA format for this):
      1. paper 1
      2. paper 2
      3. paper 3
      4. paper 4
      5. paper 5
      6. paper 6
      7. paper 7
      8. paper 8
      9. paper 9
      10. paper 10
  8. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits:
    • Record the top 10 papers (you don't need to do APA format for this):
      1. paper 1
      2. paper 2
      3. paper 3
      4. paper 4
      5. paper 5
      6. paper 6
      7. paper 7
      8. paper 8
      9. paper 9
      10. paper 10
  9. Add the word “Review” to any articles that are review articles that you listed in question 8.
  10. Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
    • Do you find any new articles that you did not find before on PubMed?
    • List up to 5 new articles that were found on the author name search:
      1. paper 1
      2. paper 2
      3. paper 3
      4. paper 4
      5. paper 5
  11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:
    • Record the top 10 papers (you don't need to use APA format for this):
      1. paper 1
      2. paper 2
      3. paper 3
      4. paper 4
      5. paper 5
      6. paper 6
      7. paper 7
      8. paper 8
      9. paper 9
      10. paper 10
  12. We will now create a shared bibliography for the entire class. Go through the search results that you have found and add articles to the class shared bibliography page.
    • Only add articles that are unique (everyone will be adding to the page and we do not want redundant articles)
    • Put review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, place it in the other articles section.
    • Add the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Add your wiki signature to the end of the citation.
    • Ideally, each student will contribute 2-3 unique articles that would be worthy of a journal club. Add articles that are related to what you are interested in investigating for the second research project.
  13. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
      • How many articles have cited the article you have been assigned?
  14. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
    • Google Scholar: advantages
    • Google Scholar: disadvantages
    • PubMed: advantages
    • Pubmed: disadvantages
    • Web of Science: advantages
    • Web of Science: disadvantages
  15. What impact does choice of keywords have on your results?
  16. For your Conclusion section, 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 what you learned that was new today.
  17. Send an e-mail to Dr. Dahlquist for team requests for the second journal club and final projects. The e-mail is due at the same time the assignment is due.
    • Name one person you do not want to work with.
    • Name three people you do want to work with.

Shared Journal Assignment

No separate shared journal assignment for this week, the class shared bibliography page will serve as the shared assignment.

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