Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
  
==April 2010 Meetings==
+
==April 2011 Meetings==
 +
 
 +
 
 +
==April 7, 2011==
 +
 
 +
 
 +
Transgene Model
 +
*On Wiki
 +
*Sent out to people
 +
*Have a look; report any concerns
 +
*Can follow on BitBucket; search for transgene; link to Wiki
 +
*No objections at Caltech; Karen will send to Paul Davis
 +
*Changes to ACE dumping script; Karen will talk to Juancarlos
 +
*Changes needed in OA (softer deadline than dump)
 +
 
 +
 
 +
Interactions
 +
*Murky genetic interaction curation?
 +
*Err on the side of generality/trusting author statements
 +
*When in doubt, curate as "genetic interaction"
 +
*Chris is working on decision tree/pipeline for curation
 +
*Kimberly working on Physical Interaction model
 +
 
 +
 
 +
BioGRID meeting at Princeton in May
 +
*Call in
 +
*What will Rose propose?
 +
 
 +
 
 +
Expression Pattern Curation (Daniela/Wen)
 +
*Daniela sent out picture page for review
 +
*Expr Pattern OA wiki is in place:
 +
**http://wiki.wormbase.org/index.php/Expression_Pattern
 +
*As soon as Juancarlos is done with the modularization will start working on the code.
 +
*In the meanwhile Daniela will curate expression pattern writing .ace files
 +
*Expr_pattern OA should be ready by the next upload (May26th).
 +
 
 +
 
 +
Patch file/Interbuild (Raymond)
 +
*Developed good patch file
 +
*Tested patch file to update WS224 to WS225 - seems OK
 +
*Less than 5 minutes for upload
 +
*Testing now should be done by Todd/OICR team
 +
 
 +
 
 +
Uma started
 +
*Working on concise descriptions of gene classes
 +
*Karen has reviewed with Uma; Uma is reading papers
 +
*Discussing details of descriptions
 +
*Inconsistencies/discrepancies of gene class names
 +
*>2400 gene classes
 +
*Can work on generating formula for this curation
 +
*Arun can help with automation
 +
*May need to get Uma an interface to enter data into postgres
 +
*Adapt concise description CGI for her?
 +
*Gene class name and a text field
 +
*Using Textpresso/WormMart output; sentence saver?
 +
 
 +
 
 +
eggNOG data into citace?
 +
*Who's going to handle the data? curate?
 +
*Michael? OK

Revision as of 22:50, 7 April 2011

2009 Meetings


2011 Meetings

February

March

April 2011 Meetings

April 7, 2011

Transgene Model

  • On Wiki
  • Sent out to people
  • Have a look; report any concerns
  • Can follow on BitBucket; search for transgene; link to Wiki
  • No objections at Caltech; Karen will send to Paul Davis
  • Changes to ACE dumping script; Karen will talk to Juancarlos
  • Changes needed in OA (softer deadline than dump)


Interactions

  • Murky genetic interaction curation?
  • Err on the side of generality/trusting author statements
  • When in doubt, curate as "genetic interaction"
  • Chris is working on decision tree/pipeline for curation
  • Kimberly working on Physical Interaction model


BioGRID meeting at Princeton in May

  • Call in
  • What will Rose propose?


Expression Pattern Curation (Daniela/Wen)

  • Daniela sent out picture page for review
  • Expr Pattern OA wiki is in place:
  • As soon as Juancarlos is done with the modularization will start working on the code.
  • In the meanwhile Daniela will curate expression pattern writing .ace files
  • Expr_pattern OA should be ready by the next upload (May26th).


Patch file/Interbuild (Raymond)

  • Developed good patch file
  • Tested patch file to update WS224 to WS225 - seems OK
  • Less than 5 minutes for upload
  • Testing now should be done by Todd/OICR team


Uma started

  • Working on concise descriptions of gene classes
  • Karen has reviewed with Uma; Uma is reading papers
  • Discussing details of descriptions
  • Inconsistencies/discrepancies of gene class names
  • >2400 gene classes
  • Can work on generating formula for this curation
  • Arun can help with automation
  • May need to get Uma an interface to enter data into postgres
  • Adapt concise description CGI for her?
  • Gene class name and a text field
  • Using Textpresso/WormMart output; sentence saver?


eggNOG data into citace?

  • Who's going to handle the data? curate?
  • Michael? OK