BIOL368/S20:Week 8

From OpenWetWare
Jump to navigationJump to search
BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

Home       People        LibGuide       Brightspace       Box       Help  

The deadline for this journal entry has been extended to Thursday, March 26, at 12:01am Pacific 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.
  • Students will be able to evaluate resources for reliability, validity, accuracy, authority, and bias.

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 the same as for the HIV Evolution Project.

Format and Content Checklist

  1. Store this journal entry as "username Week 8".
  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. Copy the questions from the assignment page and provide your answers.
  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.
    • Because this assignment is designed to find references in the literature, it is a little different than other assignments. The citations that are embedded as answers to the questions in the assignment do not need to be repeated in this section. However, you do need to cite the assignment page and any web resource pages you used to complete the assignment.

Resources

Assignment

The goal for this assignment is to create a class shared annotated bibliography of references for the next phase of the HIV research project where we will investigate the structure-function implications of mutations in the gp120 protein.

  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:
      • (your terms here)
  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.
  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. 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.
  17. 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)?
  18. 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. Read the abstract. Write 1-2 sentences about the relevance of this article to understanding the structure-function relationship of mutations in the HIV-1 gp120 protein.
    11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
    12. Copy your 1-2 sentence statement about the relevance and the recommendation (plus justification) and paste into the class shared bibliography as a bullet point underneath your assigned paper.
  19. 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 evaluating sources, and what you learned that was new that you learned today.

Example

Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568

Shared Journal Assignment

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


Retrieved from "https://openwetware.org/mediawiki/index.php?title=BIOL368/S20:Week_8&oldid=1096766"