Difference between revisions of "WormBase-Caltech Weekly Calls"

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*As soon as Juancarlos is done with the modularization will start working on the code.
 
*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
 
*In the meanwhile Daniela will curate expression pattern writing .ace files
*Expr_pattern OA should be ready by the next upload (May26th).
+
*Expr_pattern OA should be ready by the next upload (May26th). (I really doubt this, parsing in data, writing dumpers, and checking it take a long time.  Picture and Interaction each probably took longer than 2 months, and we're not starting Expr until May at the earliest -- Juancarlos)
  
  

Revision as of 22:57, 7 April 2011

2009 Meetings


2011 Meetings

February

March


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). (I really doubt this, parsing in data, writing dumpers, and checking it take a long time. Picture and Interaction each probably took longer than 2 months, and we're not starting Expr until May at the earliest -- Juancarlos)


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