2011 Advisory Board Meeting

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2011 schedule

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 tier III 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?
      • Ownership of genome assemblies? Tier IIs required to be owned by Wormbase for re-submission
    • Support for "tier IV" (transcriptome-only) / "tier V" (genome-only) worms
    • Support for "in-progress" genome projects (See also Ensembl pre-sites)
  • (Re-)sequencing
    • What should the elegans reference sequence be?
      • We have RNASeq evidence from at least four labs for about 500 to 1000 genomic errors in the reference sequence compared to 'their' N2. However each lab has a different set of errors.
      • 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) (Presentation on Prezi.com)
    • Tour of the new website (Abby; 30 minutes)
  • Process and pathway curation and display (Karen; 10 minutes)
  • Data Integration/Data Mining - WormMart & Future Perspectives (Ruihua; 10 minutes)

12:00 – 13.00 Lunch

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

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

15:00 – 15:30 Break

15:30 - 17:00: Literature Curation

  • Literature curation introducton : Gary Schindelman (update on stats) - 7-10 minutes
  • Ontology Annotator
    • Juancarlos Chan - general introduction of OA (15 min)
    • Xiaodong Wang - developing interaction OA; BioGRID (5-10 min)
  • Picture curation : Daniela Raciti - 10 minutes
  • Virtual Worm Overview : Chris Grove - 3 minutes
  • Collaboration with other Databases/Projects - automation (ARRA), GO
    • journal article processing (GSA markup) Arun, Karen (15 min)
    • Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)
    • Semi-Automated GO Curation - Exporting our Cellular Component Curation Pipeline to other MODs, Progress on Molecular Function Pipeline (Kimberly; 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 – 15:00 Post ABM Discussion

(Advisory Board not required to attend this session)

Arrivals/Departures

Arrive

  • Hinxton Crew - Pasadena Tuesday afternoon/evening?
  • Kimberly - Pasadena, Monday 1/31 evening
  • Ranjana - Tuesday, 2/1 evening

Depart

  • Hinxton Crew minus Michael - Pasadena Sunday before lunch?
  • Michael P. - Pasadena Saturday morning
  • Kimberly - Friday, 2/4 evening
  • Ranjana - Saturday afternoon