WormBase SAB Meeting
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Revision as of 04:34, 25 January 2011 by Psternberg (talk | contribs) (→13:00 – 15:30 Build, Sequence curation and analysis, other nematodes)
WormBase Scientific Advisory Board Meeting
California Institute of Technology, February 3rd - 4th 2011
Contents
Wednesday 2nd Feb – Pre-Meeting (WormBase central)
(AB not required to attend this session)
6:30 – 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) genomes
- Support for "in-progress" genome projects (c.f. Ensembl pre-sites)
- Minimal requirements for integration into WormBase(
- (Re-)sequencing
- What should the elegans reference sequence be?
- Re-sequencing a standard N2 isolate?
- 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?
- What should the elegans reference sequence be?
- (Re-)distribution of tasks within the consortium
- Array probe mapping
- RNAi target identification
- Visualisation
- GBrowse: making it -seq friendly
- Interaction browser: what shall we use?
Thursday 3rd Feb – Millikan Board Room
9:00 - 12:00: Overview, Build, Website, UI
- Introduction: Where we are; Hinxton Reorganization - (Paul Sternberg; 15 min)
- Slot for new Hinxton PIs (Paul Kersey and Matt Berriman; 30 mins)
- Build and associated topics - (Kevin Howe; 20 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
- 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 Breake
15:30 - 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)
General Discussion
- Coordination among sites
- Quality control
- Outreach
WormBook (Jane Mendel, 10 minutes)
- Database migration community annotation
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
(AB 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 PM?