Difference between revisions of "WebDev 2009.06.03-Agenda and Minutes"

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(New page: Agenda * Administrative update (Todd, 5 minutes) * Describe GFF2 -> GFF3 progress and define deadline (Norie, 10 minutes) * Discuss WormMart handling and maintenance (10 minutes) * Job...)
 
 
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Agenda
 
Agenda
  
−
* Administrative update (Todd, 5 minutes)
+
== Administrative update (Todd, 5 minutes)==
  
−
* Describe GFF2 -> GFF3 progress and define deadline (Norie, 10 minutes)
+
WS202 rollout; power failures at CSHL; all services restored.
  
−
* Discuss WormMart handling and maintenance (10 minutes)
+
== Describe GFF2 -> GFF3 progress and define deadline (Norie, 10 minutes)==
  
−
* Job candidates and schedule (10 minutes)
+
* '''Norie will have something by Friday'''.
 +
* Will email Erich and Todd, and commit changes back to repository.
 +
* Add GFF validation step (there are some problems with children with no parents in WS180 GFF3)
 +
* Contact Peter when GFF3 is available
  
−
* modENCODE status update (Marc, Peter, Zheng, 10 minutes)
+
== Discuss WormMart handling and maintenance (10 minutes)==
 +
* Zheng is running it on server at OICR: res.oicr.on.ca
 +
* We Will plan to add to update pipeline shortly.
 +
* TH:  Is there a 'Mart installation at OICR? eg: Can we host WormMart ion existing infrastrucutre?
 +
* LS: Load data into Arek's existing, externally available BioMart
 +
** Arek has dedicated existing mysql database and loads of capacity
 +
** '''Zheng will talk with Arek about hosting'''
 +
 
 +
== Job candidates and schedule (10 minutes)==
 +
 
 +
* Scheduling interviews for later this week and next
 +
 
 +
== modENCODE status update (Marc, Peter, Zheng, 10 minutes)==
 +
 
 +
* Zheng:  scripted GEO fetching
 +
* Peter: Working with LaDeana Hillier's data, this will be available on WormBase shortly.
 +
 
 +
http://modencode.oicr.on.ca/~pruzanov/cgi-bin/gbrowse/worm/?start=110643;stop=112642;ref=I;width=800;version=100;drag_and_drop=on;show_tooltips=on;grid=on;id=d6fffa28235f2a8d6befe1b569019800;label=Genes-rainbow_genelet_L2-rainbow_transcript_L2-rainbow_genelet_L3-rainbow_transcript_L3-rainbow_genelet_L4-rainbow_transcript_L4-rainbow_genelet_YA-rainbow_transcript_YA
 +
 
 +
* TH: exec function?
 +
** LS: Executes script everytime config is parsed.  If not cached, will fetch tracks from modencode, set to reload every hour.
 +
 
 +
*MP: Snyder project now has about a dozen datasets
 +
 
 +
* LS: GBrowse server farm at OICR:
 +
 
 +
Finished installing a browser server farm for modencode: gbrowse.modencode.oicr.on.ca
 +
 
 +
Load balancing system: 5 machines
 +
Two front-end load-balancing machines of 8 cores each: load balancing and rendering
 +
Two back-end machines of 8 cores each: rendering
 +
Database server with NFS
 +
 
 +
* TH: will other OICR projects be able to use this architecture?
 +
* LS: possibly ;)

Latest revision as of 10:49, 3 June 2009

Agenda

Administrative update (Todd, 5 minutes)

WS202 rollout; power failures at CSHL; all services restored.

Describe GFF2 -> GFF3 progress and define deadline (Norie, 10 minutes)

  • Norie will have something by Friday.
  • Will email Erich and Todd, and commit changes back to repository.
  • Add GFF validation step (there are some problems with children with no parents in WS180 GFF3)
  • Contact Peter when GFF3 is available

Discuss WormMart handling and maintenance (10 minutes)

  • Zheng is running it on server at OICR: res.oicr.on.ca
  • We Will plan to add to update pipeline shortly.
  • TH: Is there a 'Mart installation at OICR? eg: Can we host WormMart ion existing infrastrucutre?
  • LS: Load data into Arek's existing, externally available BioMart
    • Arek has dedicated existing mysql database and loads of capacity
    • Zheng will talk with Arek about hosting

Job candidates and schedule (10 minutes)

  • Scheduling interviews for later this week and next

modENCODE status update (Marc, Peter, Zheng, 10 minutes)

  • Zheng: scripted GEO fetching
  • Peter: Working with LaDeana Hillier's data, this will be available on WormBase shortly.

http://modencode.oicr.on.ca/~pruzanov/cgi-bin/gbrowse/worm/?start=110643;stop=112642;ref=I;width=800;version=100;drag_and_drop=on;show_tooltips=on;grid=on;id=d6fffa28235f2a8d6befe1b569019800;label=Genes-rainbow_genelet_L2-rainbow_transcript_L2-rainbow_genelet_L3-rainbow_transcript_L3-rainbow_genelet_L4-rainbow_transcript_L4-rainbow_genelet_YA-rainbow_transcript_YA

  • TH: exec function?
    • LS: Executes script everytime config is parsed. If not cached, will fetch tracks from modencode, set to reload every hour.
  • MP: Snyder project now has about a dozen datasets
  • LS: GBrowse server farm at OICR:

Finished installing a browser server farm for modencode: gbrowse.modencode.oicr.on.ca 

Load balancing system: 5 machines
Two front-end load-balancing machines of 8 cores each: load balancing and rendering
Two back-end machines of 8 cores each: rendering
Database server with NFS
  • TH: will other OICR projects be able to use this architecture?
  • LS: possibly ;)
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