Difference between revisions of "Rlegaspi Week 11"

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(Fixing template on the page.)
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{{Heavy Metal Haterz}}
 
{{Heavy Metal Haterz}}
  
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'''This journal entry is due on Tuesday, November 17, at midnight PST.''' ''(Monday night/Tuesday morning)''
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= Journal Club Preparation: Microarray Paper =
  
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== Overview ==
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== Bibliographic Information of Microarray Paper ==
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Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. ''BMC genomics, 10''(1), 131.
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*The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed/?term=Yang%2C+Y.%2C+Harris%2C+D.+P.%2C+Luo%2C+F.%2C+Xiong%2C+W.%2C+Joachimiak%2C+M.%2C+Wu%2C+L.%2C+...+%26+Zhou%2C+J.+%282009%29.+Snapshot+of+iron+response+in+Shewanella+oneidensis+by+gene+network+reconstruction.+BMC+genomics%2C+10%281%29%2C+131. PubMed].
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*The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667191/ PubMedCentral]
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*The link to the full text of the article (HTML format) from the publisher [http://www.biomedcentral.com/1471-2164/10/131 web site].
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*The link to the full [http://www.biomedcentral.com/content/pdf/1471-2164-10-131.pdf PDF] version of the article from the publisher web site.
  
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For this week, your team has two main tasks:
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== Defining Unfamiliar Biological Terms ==
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Task Description: Made a list of at least 10 biological terms for which I did not know the definitions when I first read the article.  Defined each of the terms.  Yse 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.'''''
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# Prepare for journal club presentations in Weeks 12 and 13
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#* You will deeply explore and perform a critical review of the genome paper (coder/QA) and microarray paper (GenMAPP users) for your team's species.
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#* You will communicate your findings in an effective oral presentation.
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# Begin initial tasks on your research project
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#* Coder/QA
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#** Set up coding/testing environment
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#** Determine the regular expression for the ordered locus ID for your species
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#** Identify the appropriate model organism database for your species.
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#** Perform an initial Gene Database export and Gene Database Testing Report
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#* GenMAPP Users
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#** Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
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#** Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
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#** Compile the raw data in preparation for normalization and statistical analysis.
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== Individual Journal Assignment ==
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* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
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* Link from your user page to this Assignment page.
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* Link to your journal entry from your user page.
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* Link back from your journal entry to your user page.
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* Link from your journal entry to your team's home page.
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* Link from your team's home page to your journal entry.
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* Don't forget to add the categories "Journal Entry", "Group Projects", and your team's category to the end of your wiki page.
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**'''''Note: you can easily fulfill all of these links by adding them to your template (and your team's template) and then using your template on your journal entry.'''''
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* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week.  An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
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=== Preparation for Journal Club on Your Species ===
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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.
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In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
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# 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.'''''
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# 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.
 
# 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 is the importance or significance of this work (i.e., your species)?
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#*# Construct a flow chart that illustrates the above.
 
#*# Construct a flow chart that illustrates the above.
  
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=== Journal Club Presentation ===
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<!-- === 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.   
 
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.   
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*# What are the best points about the presentation's organization, visuals, and delivery?  Please give at least 2 specific examples.
 
*# What are the best points about the presentation's organization, visuals, and delivery?  Please give at least 2 specific examples.
 
*# What points need improvement? Please give at least 2 specific examples.
 
*# What points need improvement? Please give at least 2 specific examples.
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* 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.
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* 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.  
  
 
== Team Journal Assignment ==
 
== Team Journal Assignment ==
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** Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
 
** Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
 
* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
 
* Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
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* Set up a system for managing team files, including a filename system that keeps track of versions of files.
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* Set up a system for managing team files, including a filename system that keeps track of versions of files. -->
  
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[[Category:Assignment]]
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= Links to User Page and Journal Pages =
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[[Category:Group Projects]]
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{{Template:Rlegaspi}}
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[[Category:Heavy Metal HaterZ]]

Revision as of 09:52, 12 November 2015

HeavyMetal.jpg

Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

Important Links

Our Files

Our Deliverables

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors
Individual Journal Entries
Mary Alverson Week 11 Week 12 Week 14 Week 15
Emily Simso Week 11 Week 12 Week 14 Week 15
Ron Legaspi Week 11 Week 12 Week 14 Week 15
Josh Kuroda Week 11 Week 12 Week 14 Week 15

Journal Club Preparation: Microarray Paper

Bibliographic Information of Microarray Paper

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC genomics, 10(1), 131.

  • 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.

Defining Unfamiliar Biological Terms

Task Description: Made a list of at least 10 biological terms for which I did not know the definitions when I first read the article. Defined each of the terms. Yse 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.

  1. 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.


Links to User Page and Journal Pages

Ron Legaspi
BIOL 367, Fall 2015

Assignment Links
Individual Weekly Journals
Shared Weekly Journals
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