Difference between revisions of "WormBase SAB Meeting"
Line 22: | Line 22: | ||
==Monday 28th Jan == | ==Monday 28th Jan == | ||
− | === 9:00 - | + | === 9:00 - 9:15 Overview === |
* Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min) | * Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min) | ||
− | + | ||
+ | === 9:15 - 10:30 Website / User interface === | ||
+ | |||
** Site introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes) | ** Site introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes) | ||
** Tour of the new website (Abby; 20 minutes) | ** Tour of the new website (Abby; 20 minutes) | ||
** Intermine introduction, status, and goals (JD; 15 minutes) | ** Intermine introduction, status, and goals (JD; 15 minutes) | ||
− | * | + | === 10:30 - 10:45 Coffee break === |
− | * | + | |
+ | === 10:45 - 12:15 Nematode genomes and transcriptomes === | ||
+ | |||
+ | * Coping with the explosion of nematode sequence data (Kevin; 20 mins) | ||
+ | * Sequence curation - current status and future plans (Paul; 20 mins) | ||
+ | * RNASeq data in WormBase | ||
+ | ** Alignment and annotation pipeline (Gary; 10 mins) | ||
+ | ** SPELL (Wen; 10 mins) | ||
+ | * Annotation of Brugia malayi - a pilot study for future WormBase community interactions (Michael; 20 mins) | ||
=== 10:30 - 10:40 -- COFFEE === | === 10:30 - 10:40 -- COFFEE === |
Revision as of 13:52, 16 January 2013
WormBase_Consortium Scientific Advisory Board Meeting
California Institute of Technology, January 27-29, 2013
Contents
Advisors list
Sunday 27th Jan – Pre-Meeting (WormBase central)
(Advisory Board not required to attend this session)
- Revive GFF3 production/testing
- Representation of multiple assemblies for a single species (on web-site and FTP site)
- Mechanism to stage/review changes to static content without immediately publishing it to live site
- Future web-site features
- Incremental updates
- Data that we produce that cannot currently be viewed on web-site
- Multiple and pairwise genomic alignments
- Nematode gene trees
Monday 28th Jan
9:00 - 9:15 Overview
- Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min)
9:15 - 10:30 Website / User interface
- Site introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes)
- Tour of the new website (Abby; 20 minutes)
- Intermine introduction, status, and goals (JD; 15 minutes)
10:30 - 10:45 Coffee break
10:45 - 12:15 Nematode genomes and transcriptomes
- Coping with the explosion of nematode sequence data (Kevin; 20 mins)
- Sequence curation - current status and future plans (Paul; 20 mins)
- RNASeq data in WormBase
- Alignment and annotation pipeline (Gary; 10 mins)
- SPELL (Wen; 10 mins)
- Annotation of Brugia malayi - a pilot study for future WormBase community interactions (Michael; 20 mins)
10:30 - 10:40 -- COFFEE
- Monday afternoon
- Literature curation workflow and tools (50)
- Towards Integrated Phenotype Curation (30)
- Interactions (20)
- GO (20)
- Cell Function (10)
- Processes and pathways (20)
- ??Transcriptional Networks:
- Revisiting tools with respect to Community Annotation (40)
- Acedb migration (20 Kevin and Todd)
Monday morning Website: status, plans, and how much we can accomplish. (60) Todd, Abby WormMine (30) JD Many Genomes (60) Hinxton Many Transcriptomes (30) [incl. Wen on SPELL]
Monday afternoon Literature curation workflow and tools (30). Towards Integrated phenotype curation: (alleles, RNAi, transgenes, interactions, GO (40). Gene expression and regulation: Transcriptional Networks (Xioadong, Daniela) Community Annotation (30): Concise descriptions [Kimberly, Ranjana]; Human disease Processes and pathways (30). Karen Community Annotation wikiPathways [Karen]; Community Annotation: by webforms with focus on specific types Community Annotation gene models?; Acedb migration (20) Websites pages for other species
BELOW IS OLD STUFF:
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)
- Minimal requirements for integration into WormBase
- (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?
- What should the elegans reference sequence be?
- (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