Difference between revisions of "Week 11"

Revision as of 06:52, 7 November 2017

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 14 and Tuesday, November 21. The Coders (and Designer) will present first on November 14, while the QA's and Data Analysts will present second on November 21.

Paper assignments:

• Design team: Liikkanen, L. A. (2017). The data-driven design era in professional web design. interactions, 24(5), 52-57. DOI: 10.1145/3121355
• Four API's team: Ford, P. (2015). What is Code? Part 5: The Time You Attended the E-mail Address Validation Meeting. Bloomberg Businessweek (June 11, 2015).
• JASPAR team: Ford, P. (2015). What is Code? Part 6: How Are Apps Made? Bloomberg Businessweek (June 11, 2015).
• Interaction and Integration team: Meyer, R. (2015). The secret startup that saved the worst website in America. The Atlantic (July 9, 2015).

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 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 an in text citation that corresponds to an entry in you References section. Use APA formatting and provide a hyperlink to the URL if it is a web citation. Each definition must have it's own citation, even if you used the same overall source.
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 at 100% scale 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 main message of this work?
   • What is the importance or significance of this work?
   • What were the methods used in the study (if any)?
   • Briefly state the result shown in each of the figures and tables (if any).
   • Summarize the main points of the paper.
   • What aspects of this paper will inform how you carry out your final project?

Journal Club Presentation

The Coders (and Designer) will prepare and give a 15 minute PowerPoint presentation for their paper in class on Tuesday, November 14.

• 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 12:01am, Tuesday, November 14.
  • 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 is the best thing about this presentation?
  3. What needs improvement?
  4. Please comment on the speaking style (language and delivery) of each presenter.
• 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 one.

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

• 1. • 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:
         • EBI ArrayExpress (recommended)
           • Click on the link to "Browse ArrayExpress"
           • Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
         • NCBI GEO
         • Stanford Microarray Database
         • PUMAdb (Princeton Microarray Database)
         • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
     • 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.

-->

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
• Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
• Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
• Publisher: American Society for Cell Biology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no

-->

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.

1. 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 organize your work and 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.
2. Create a link to your team's page on the course Main page.
3. Create a template for your team with useful information and links that you will invoke on all pages that you will create for the project.
   • Create a category using your team name and include it on your team's template so that it also gets used on all pages you will create for the project. Also use include the category "Group Projects" in your template.
     • However, please do not add these categories to your own individual templates because we want them to precisely mark pages having to do with the Group Projects and your team, respectively.
4. Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
5. Each team member should reflect on the team's progress:
   1. What worked?
   2. What didn't work?
   3. What will I do next to fix what didn't work?
6. Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.