Difference between revisions of "Kzebrows Week 11"

Revision as of 23:03, 12 November 2015

Preparation for Journal Club on Your Species

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.

Guild Meeting Notes 11/10: GenMAPP Users

1. Experimental design (for sure do by next week)
   • Treatment vs. control
   • Biological vs. technical replicates: which one and how many
     • Biological replicates: independent samples
     • Technical replicates: if at any point sample is split into two and treated differently
     • NOTE: should be able to find # chips or microarrays (a combo of the above should add up to this)
   • dye swaps: green and red dye behave differently in experiments
     • Figure out how many dye swaps occurred (best is even, but they could have done half and half and swapped it or used technical replicates)
   • Flow chart (will go into final paper and presentation!)
2. Sample and data relationships: Match each chip/filename with a sample. One file should correspond to one chip. (look at by next week)
   • raw.zip should have the files in it
   • sdrf.txt (Sample Data Relationship File) spreadsheet
   • NOTE: Double-check with Dr. Dahlquist
3. Create compiled raw data file with ID, sample log 2 fold, sample log size, etc.
4. Normalization and stats (scaling and centering data, calculating T tests and B-H/Bonferroni corrections). Can consult with Dr. Dahlquist for customized procedure.
   • Goal: do a sanity check and compare to what was actually written in the paper to see if it matches (probably not identical but same magnitude and direction)
5. GenMAPP: format data and run through GenMAPP and MAPPFinder (converge here with Coder and QA)
   • Do biological interpretation of the data, analyze, and find out something new because the paper did not have this kind of analysis previously
   • Identify exceptions and feed info back to QA person (a few hundred is ok, just hopefully not more than 10% of genome)

Deliverables: responsible for describing methods, how raw data file was found, etc., data tables, GenMAPP and MAPPFinder analysis and interpretation. Compare or contrast in discussion what was found vs. what coder and QA found.

Team Meeting Notes 11/12