BIOL368/F20:Week 3

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Fall 2020

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This journal entry is due on Thursday, September 24, at 12:01am Pacific time.


Overview

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 the first research project.
  • To learn how to do a journal club presentation.

Individual Journal Assignment

You will be able to earn back the points you missed on the Week 1 assignment by making the changes listed below by the Week 3 deadline on 12:01 am, Thursday, September 24.

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:
    • Figure 1A & 1B: Fatima & Kam
    • Figure 1C & 1D: Nathan & Owen
    • Figure 2: Aiden & Macie
    • Figure 3: JT & Ian
    • Figure 4A & 4B: Anna & Taylor
    • Figure 4C: Yaniv & Nida

Format and Content Checklist

  1. Store this journal entry as "username Week 3" (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 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.

Background

Preparation for Journal Club 1

The paper we will read for Journal Club 1 is:

"Science... is a process taking place in the minds of living scientists," (Curtis, 1983). The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings are others). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research. This is the first of two journal club discussions we will have this semester. For this first journal club, the entire class will read and present the same paper referenced above. Each student will create an individual wiki journal page for his or her Week 3 assignment and also contribute to the shared journal page in preparation for the presentation in class on the Thursday of Week 4.

  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 goals and results of previous studies that led them to perform this work?
    • What is the main result presented in this paper? (Hint: look at the few sentences of the introduction and restate them 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.
    • What light does their work shed on the origin of the SARS-CoV-2 virus (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. Each pair of students will be assigned a table and/or figure. You will be responsible for explaining the table/figure in detail to the class, including the methods used to obtain that figure/table. The instructor will provide the PowerPoint presentation slides containing the figures and tables you will present.
    • Figure 1A & 1B: Fatima & Kam
    • Figure 1C & 1D: Nathan & Owen
    • Figure 2: Aiden & Macie
    • Figure 3: JT & Ian
    • Figure 4A & 4B: Anna & Taylor
    • Figure 4C: Yaniv & Nida

Online Biological Dictionaries

How to Read a Primary Research Article

A primary research article is divided into sections that each have a different purpose. Articles in Science and Nature are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there.

Abstract

The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on PubMed and may be the only part of the text publicly available.

Introduction

The introduction gives the background information necessary to understand the paper. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

Funnel.jpg
  • States importance of the problem
  • States what is known about the problem
  • States what is unknown about the problem
  • States clues that suggest how to approach the unknown
  • States the question the paper is trying to address
  • States the experimental approach
  • Sometimes briefly states the answer they found

Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.

Results

Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.

Discussion

States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.

References

List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor (Let the buyer beware)

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

Shared Journal Assignment

  • Compose your journal entry in the shared Class Journal Week 3 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

Answer the following questions on the Class Journal Week 3 page after you have completed the individual assignment.

  1. What aspect of this assignment came most easily to you?
  2. What aspect of this assignment was the most challenging for you?
  3. What (yet) do you not understand?
  4. What are you wondering about regarding the journal club article that might become the basis for a research project?