Difference between revisions of "WormBase SAB Meeting"

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'''13:00''' – Discussion
 
'''13:00''' – Discussion
  
<b>(Advisory Board not required to attend this session)</b>
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'''(Advisory Board not required to attend this session)'''
  
 
== Arrivals/Departures ==
 
== Arrivals/Departures ==

Revision as of 11:32, 26 January 2011

WormBase_Consortium Scientific Advisory Board Meeting

Caltechlogo.gif
California Institute of Technology, February 3rd - 4th 2011

Wednesday 2nd Feb – Pre-Meeting (WormBase central)

(Advisory Board not required to attend this session)

9:00 - 9:15 delegates arrive

9:15 - 9:30 pre-pre-meeting coffee

9:30 – 18:00 Put right the World

Potential Discussion topics

  • Release cycle

    • Implications of less frequent releases
    • Strategies for "as live" display of certain data types

  • Gene-structure curation

    • Manual versus automatic-RNASeq-guided (and how we might do the latter)
    • Which genomes should be manually curated?
    • Community annotation of tierIII genomes
    • Should we invest resources into "semi-automatic" annotation of 3rd party genomes?

  • New species

    • Minimal requirements for integration into WormBase(
      • Submission to ENA/Genbank? Gene-set?
    • Support for "tier IV" (transcriptome-only) / "tier V" (genome-only) worms
    • Support for "in-progress" genome projects (cf Ensembl pre-sites)

  • (Re-)sequencing

    • What should the elegans reference sequence be?
      • Re-sequencing a standard N2 isolate and make available from CGC.
        • This has been discussed and proposed a number of times, but has never progressed from "That's a really good idea" :(
        • Requires willing lab to prep large number of samples
        • Requires money for new tech seq run
    • Handling 1000s of elegans mutant and wild isolate strain genomes?
      • Representation of non-reference variants of genes/features etc.
    • Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?

  • (Re-)distribution of tasks within the consortium

    • Array probe mapping
    • RNAi target identification
    • C.elegans monthly clone submission

  • Visualisation

    • GBrowse: making it -seq friendly
    • Interaction browser: what shall we use?

  • website development

    • implications of freeze on current website development - should we make this public?
    • will existing developments be incorporated into new website at start?

Thursday 3rd Feb – Millikan Board Room

9:00 - 12:00: Overview, Website / UI

  • Introduction: Where we are; Hinxton Reorganization - (Paul Sternberg; 15 min)
  • Slot for new Hinxton PIs (Paul Kersey and Matt Berriman; 30 mins)
  • User interface
    • Site usage; introduction to the new site (Todd; 30 minutes)
    • Tour of the new website (Abby; 30 minutes)
  • Process and pathway curation and display (Karen; 10 minutes)
  • Data Integration/Data Mining - WormMart (Ruihua; 10 minutes)

13:00 – 15:00 Build, Sequence curation and analysis, other nematodes

  • Build update - Kevin Howe (20 mins)
  • C. elegans(+ Tier II) Manual curation and projects? - Paul D. (20 mins)
  • Genetic data - Mary Ann (presented by a Hinxton surrograte; 15 mins)
  • Non-elegans species - an update - Michael/Kevin (15 mins)
  • Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
    • microarray and SPELL -Wen C. (5 min)
  • Tier II genome (re)submissions

15:00 – 15:30 Break

15:30 - 17:00: Literature Curation

  • Literature curation introducton : Gary Schindelman (update on stats) - 5 minutes
  • Ontology Annotator
    • Juancarlos Chan - general introduction of OA
    • Xiaodong Wang - developing interaction OA
  • Picture curation : Daniela Raciti - 10 minutes
  • Virtual Worm Overview : Chris Grove - 2 minutes
  • Gene Function Curation - concise descriptions (update on numbers, curation approach)
  • Collaboration with other Databases/Projects - automation (ARRA), BioGRID, GO
    • GSA Arun/Karen
    • Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)
  • WormBook (Jane Mendel, 10 minutes)

17:00 - 17:30: General Discussion

  • to be determined during talks

Friday 4th Feb – Millikan Board Room

8:30 – 9:00 Advisors breakfast

9:30 – 12:00 Advisors summary report

12:00 – 13:00 Lunch

13:00 – Discussion

(Advisory Board not required to attend this session)

Arrivals/Departures

Arrive

  • Hinxton Crew - Pasadena Tuesday afternoon/evening?


Depart

  • Hinxton Crew minus Michael - Pasadena Sunday before lunch?
  • Michael P. - Pasadena Friday lunch?