Malverso Week 11
From LMU BioDB 2015
Revision as of 02:45, 16 November 2015 by Malverso (Talk | contribs) (added questions for journal club)
Contents
Personal Goals
- Prepare for journal club presentations
- Set up coding/testing environment
- Determine the regular expression for the ordered locus ID for your species
- Identify the appropriate model organism database for your species.
- Perform an initial Gene Database export and Gene Database Testing Report
Electronic Journal
- After struggling to find a Model Organism Gene Database for Shewanella oneidensis, I asked Dr.Dahlquist for assistance.
- The only database link we could find was broken.
- We decided that our next plan of action would be to use the website bacteria.ensembl.org as our MOD.
Journal Club Presentation
- 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.
- 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:
- 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])?
- What individual or organization maintains the database?
- What is their funding source(s)?
- Is there a license agreement or any restrictions on access to the database?
- How often is the database updated?
- Are there links to other databases?
- Can the information be downloaded?
- In what file formats?
- 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?
- 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_####).
Team Page
Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
Individual Journal Entries
- Malverso User Page (Week 1)
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
