Difference between revisions of "Week 11"

From LMU BioDB 2013
Jump to: navigation, search
(added note about grading/points; commented out option to add to week 10 page)
(Journal Club on Your Species: edited outline instructions, created separate header for oral presentation)
Line 18: Line 18:
 
* Continue to add useful items to your team's pages.
 
* Continue to add useful items to your team's pages.
  
=== Journal Club on Your Species ===
+
=== Preparation for Journal Club on Your Species ===
  
In preparation for the Journal Club next week, your team will complete the following assignment.  You may wish to create a subpage of your team's wiki to complete this assignment, but please provide a link on your team's home page.
+
In preparation for the Journal Club on Thursday, November 7, you will each individually complete the following assignment on your individual journal page.
 
# 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.'''''
 
# 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 the equivalent of 2 pages of standard 8 1/2 by 11 inch paper.  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)?
 
#* What were the methods used in the study?
 
#* What were the methods used in the study?
 
#* Briefly state the result shown in each of the figures and tables.
 
#* 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).
 
#* How do the results of this study compare to the results of previous studies (See Discussion).
#* In addition to the journal article, please find and review the Model Organism Database (MOD) for your species.  In particular, make sure that you can answer the following:
+
#* In addition to the journal article, please find and review the Model Organism Database (MOD) for your species.  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 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 individual or organization maintains the database?   
Line 41: Line 41:
 
#*#* Run a sample query.  Do the results make sense?
 
#*#* 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?  (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).
 
#*# What is the format (regular expression) of the main type of gene ID for this species?  (for example, for ''Vibrio cholerae'' it was VC#### or VC_####).
# Upload your completed PowerPoint slides to your team's journal page by the Week 11 journal deadline (you may make changes before your presentation Tuesday afternoon, but we will be evaluating the presentation you upload.)
+
 
 +
=== Team Journal Club Presentation ===
 +
 
 +
# Upload your completed PowerPoint slides to your team's journal page by the Week 11 journal deadline (you may make changes before your presentation on Thursday morning, but we will be evaluating the presentation you upload.)
 
#* For your PowerPoint presentation, 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.
 
#* For your PowerPoint presentation, 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.
 
#* The length of your presentation should be about 15 minutes.
 
#* The length of your presentation should be about 15 minutes.

Revision as of 18:45, 18 October 2013

Under Construction

The content in this page has not been finalized and is still subject to change. Use the current information at your own risk.

This journal entry is due on Thursday, November 7, at midnight PST. (Thursday night/Friday morning) Note different due date.

A note on the grading for this assignment:

  • The individual journal entry containing the vocabulary definitions and article outline is worth a total of 10 points. Students will be graded on an individual basis for this portion of the assignment.
  • The presentation is worth a total of 30 points; each member of the group will receive the same grade for this portion of the assignment.

Individual Journal Assignment

  • 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).
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Don't forget to add the "Journal Entry" category to the end of your wiki page.
    • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.


Team Journal Assignment

Team Wiki Pages

  • Please make any requested changes to your team's wiki pages.
  • Continue to add useful items to your team's pages.

Preparation for Journal Club on Your Species

In preparation for the Journal Club on Thursday, November 7, 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).
    • In addition to the journal article, please find and review the Model Organism Database (MOD) for your species. 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? (for example, for Vibrio cholerae it was VC#### or VC_####).

Team Journal Club Presentation

  1. Upload your completed PowerPoint slides to your team's journal page by the Week 11 journal deadline (you may make changes before your presentation on Thursday morning, but we will be evaluating the presentation you upload.)
    • For your PowerPoint presentation, 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.
    • The length of your presentation should be about 15 minutes.
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox