WormBase SAB Meeting

WormBase_Consortium Scientific Advisory Board Meeting

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

15:30 - 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?