Week 11

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This journal entry is due on Tuesday, November 14, at 12:01 PST. (Monday night/Tuesday morning)

Overview

The objectives of this week's exercise is based on your assigned role on your team:

  • Everyone will contribute to Creating your team's home page, and in the process, getting yourselves organized for the final project.
  • Coders (and Designer) will then move on to preparing a journal club presentation for Tuesday, November 14 on their assigned papers.
  • QA's and Data Analysts will search the literature and microarray databases for additional papers on the transcriptional response to cold shock in yeast. (They will prepare their journal club presentations on one of these papers for the Week 12 assignment and deliver the presentation itself on Tuesday, November 21.)

Grading for this assignment

  • Your individual journal entry for this week is worth a total of 10 points.
  • Your team journal entry for this week is also worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.
  • The journal club presentation (whether delivered on November 14 or 21) will be worth a total of 40 points.

Individual Journal Assignment

  • 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).
  • Invoke your template on your journal entry page so that you:
    • Link from your journal entry page to this Assignment page.
    • Link from your journal entry to your user page.
    • Add the "Journal Entry" category to the end of your wiki page.
  • Because you have invoked your template on your user page, you should also have a:
    • Link from your user page to this Assignment page.
    • Link to your journal entry from your user page.
  • Note that this week, we will add two new categories, "Group Projects" and a category for your team's name. Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.
  • Include both the Acknowledgments and References section as specified by the Week 1 assignment.
  • For your assignment this week, electronic laboratory notebook will be modified to fit the assignment that is specific to your role on your team.

Team Membership

  • Design team: (data analyst), (QA/PM), (designer), (coder)
  • Four API's team: (data analyst), (QA/PM), (coder), (coder)
  • JASPAR team: (data analyst), (QA/PM), (coder), (coder)
  • Interaction and Integration team: (data analyst), (QA/PM), (coder), (coder)

Coders and Designer: Prepare a Journal Club Presentation for Your Assigned Paper

Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 17 and Tuesday, November 24. The Coder and Quality Assurance person will present the genome paper for your species and the GenMAPP Users will present the microarray paper for your species. You will decide within your team who will present on which day. Please edit the schedule on the Main Page to show who is presenting on which day.

In preparation for your journal club presentation, you will each individually complete the following assignment on your individual journal page.

  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. 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 URL citation.
  2. Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see 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.
    • What is the importance or significance of this work (i.e., your species)?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
    • For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the NAR assignment. In particular, make sure to answer the following:
      1. What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
      2. What individual or organization maintains the database?
      3. What is their funding source(s)?
      4. Is there a license agreement or any restrictions on access to the database?
      5. How often is the database updated?
      6. Are there links to other databases?
      7. Can the information be downloaded?
        • In what file formats?
      8. Evaluate the “user-friendliness” of the database.
        • Is the Web site well-organized?
        • Does it have a help section or tutorial?
        • Run a sample query. Do the results make sense?
      9. What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
    • For the microarray paper (GenMAPP Users only), include the following:
      1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
      2. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
      3. Construct a flow chart that illustrates the above.

Journal Club Presentation

Each pair of students will prepare and give a 15 minute PowerPoint presentation for their paper in class on Tuesday, November 17 or Tuesday, November 24.

  • Please follow the Presentation Guidelines for how to format your slides.
  • You will need to prepare ~15 slides (assume 1 slide per minute of presentation).
  • You need to present the information in the outline of your journal article listed above, but organized as a presentation.
    • Specifically, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.
  • Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by midnight, Tuesday, November 17, even if you are presenting the following week.
    • You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
  • Your presentation (both the slides and the oral presentation) will be evalutated by the instructors using the Presentation Rubric.
  • Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
    1. What is the speaker's take-home message (one short sentence)?
    2. What are the best points about the presentation's organization, visuals, and delivery? Please give at least 2 specific examples.
    3. What points need improvement? Please give at least 2 specific examples.
  • Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this presentation.

QA's and Data Analysts: Annotated Bibliography of Papers that Contain Microarray Data from Yeast Subjected to Cold Shock

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

  • On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
  • On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
    1. The journal article which describes the results of the whole genome sequencing for your species. (Note that you will be giving a journal club presentation on this article for your Week 11 assignment.)
      • Use a keyword search for each of these databases/tools and answer the following:
        • PubMed
          • What original keyword(s) did you use? How many results did you get?
          • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • Google Scholar
          • What original keyword(s) did you use? How many results did you get?
          • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • Web of Science
          • What original keyword(s) did you use? How many results did you get?
          • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • Use the advanced search functions for each of these three databases/tools and answer the following:
        • PubMed
          • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • Google Scholar
          • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • Web of Science
          • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • Each of the references in your bibliography needs to have the following information (an example is given in another section below):
        • The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
        • The link to the abstract from PubMed.
        • The link to the full text of the article in PubMedCentral.
        • The link to the full text of the article (HTML format) from the publisher web site.
        • The link to the full PDF version of the article from the publisher web site.
        • Who owns the rights to the article?
          • Does the journal own the copyright?
          • Do the authors own the copyright?
          • Do the authors own the rights under a Creative Commons license?
          • Is the article available “Open Access”?
        • What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here.
        • Is this article available in print or online only?
        • Has LMU paid a subscription or other fee for your access to this article?
          • A list of the journals LMU pays for access to can be found here.
    2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
      • Give an overview of the results of the search.
        • How many articles does this article cite?
        • How many articles cite this article?
        • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
    3. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
      • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
        • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
        • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
        • The control sample needs to be derived from mRNA and not genomic DNA.
        • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
      • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
      • State what you used as search terms and what type of search terms they were.
      • Give an overview of the results of the search.
        • How many results did you get?
        • Give an assessment of how relevant the results were.
      • For each article, please provide all of the same information that you provided for the genome article above.
      • In addition, you must also link to the web site where the microarray data resides.
        • For each of the microarray articles/datasets, answer the following:
          1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
          2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
        • Remember, microarray data is not centrally located on the web. Some major sources are:
      • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.


Whole Team Journal Assignment: Creating a Team Wiki Page

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.

  • Name your team and create your team home page on the wiki.
    • The name of your team home page should simply be the team name.
    • This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
    • Create a link to your team's page on the course Main page.
    • Create a category using your team name and use it on your team's main page and all pages you will create for the project. Also use the category "Group Projects" on your team's pages.
    • Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
  • You will be directed to add specific information to your team's pages in this and future assignments.
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