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− | <center><b>
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− | <font size="5" color="Blue">[[WormBase_Consortium]] Scientific Advisory Board Meeting
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− | [[File:Caltechlogo.gif|frame|none]]California Institute of Technology, January 27-29, 2013 | + | = Meeting list = |
− | </font>
| + | [[2018_Advisory_Board_Meeting | 2018 SAB Meeting]] |
− | </b></center>
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− | __TOC__
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− | ===[[WormBase_Consortium#Scientific_Advisory_Board |Advisors list]]===
| + | [[2016_Advisory_Board_Meeting | 2016 SAB Meeting]] |
− | ==Sunday 27th Jan – Pre-Meeting (WormBase central)==
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− | '''(Advisory Board not required to attend this session)'''
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− | * Revive GFF3 production/testing
| + | [[2014_Advisory_Board_Meeting | 2014 SAB Meeting]] |
− | * Representation of multiple assemblies for a single species (on web-site and FTP site)
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− | * Mechanism to stage/review changes to static content without immediately publishing it to live site
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− | * Brainstorm new web-site features.
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− | ** Data that we produce that cannot currently be viewed on web-site
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− | *** Multiple and pairwise genomic alignments
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− | *** Nematode gene trees
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− | ==Monday 28th Jan ==
| + | [[2013_Advisory_Board_Meeting | 2013 SAB Meeting]] |
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− | === 9:00 - 10:30: Overview, Website / UI ===
| + | [[2011_Advisory_Board_Meeting | 2011 SAB Meeting]] |
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− | * Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min)
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− | * Website: status, plans, and how much we can accomplish. (60)
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− | ** Site introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes)
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− | ** Tour of the new website (Abby; 20 minutes)
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− | ** Intermine introduction, status, and goals (JD; 15 minutes)
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− | *Many Genomes (50)
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− | *Transcriptome data (30)
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− | === 10:30 - 10:40 -- COFFEE ===
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− | **Monday afternoon
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− | *Literature curation workflow and tools (50)
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− | *Towards Integrated Phenotype Curation (30)
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− | *Interactions (20)
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− | *GO (20)
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− | *Cell Function (10)
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− | *Processes and pathways (20)
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− | *??Transcriptional Networks:
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− | *Revisiting tools with respect to Community Annotation (40)
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− | *Acedb migration (20 Kevin and Todd)
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− | Monday morning
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− | Website: status, plans, and how much we can accomplish. (60) Todd, Abby
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− | WormMine (30) JD
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− | Many Genomes (60) Hinxton
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− | Many Transcriptomes (30) [incl. Wen on SPELL]
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− | Monday afternoon
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− | Literature curation workflow and tools (30).
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− | Towards Integrated phenotype curation: (alleles, RNAi, transgenes, interactions, GO (40).
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− | Gene expression and regulation: Transcriptional Networks (Xioadong, Daniela)
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− | Community Annotation (30): Concise descriptions [Kimberly, Ranjana];
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− | Human disease
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− | Processes and pathways (30). Karen
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− | Community Annotation wikiPathways [Karen];
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− | Community Annotation: by webforms with focus on specific types
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− | Community Annotation gene models?;
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− | Acedb migration (20)
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− | Websites pages for other species
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− | BELOW IS OLD STUFF:
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− | ==Wednesday 2nd Feb – Pre-Meeting (WormBase central)==
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− | '''(Advisory Board not required to attend this session)'''
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− | <b>9:00 - 9:15 </b>delegates arrive
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− | <b>9:15 - 9:30 </b>pre-pre-meeting coffee
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− | <b>9:30 – 18:00</b> Put right the World
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− | Potential Discussion topics
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− | * <b>Release cycle</b>
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− | ** Implications of less frequent releases
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− | ** Strategies for "as live" display of certain data types
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− | * <b>Gene-structure curation</b>
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− | ** Manual versus automatic-RNASeq-guided (and how we might do the latter)
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− | ** Which genomes should be manually curated?
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− | ** Community annotation of tier III genomes
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− | ** Should we invest resources into "semi-automatic" annotation of 3rd party genomes?
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− | * <b>New species</b>
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− | ** Minimal requirements for integration into WormBase
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− | *** Submission to ENA/Genbank? Gene-set?
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− | *** Ownership of genome assemblies? Tier IIs required to be owned by Wormbase for re-submission
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− | ** Support for "tier IV" (transcriptome-only) / "tier V" (genome-only) worms
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− | ** Support for "in-progress" genome projects (See also [http://pre.ensembl.org/index.html Ensembl pre-sites])
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− | * <b>(Re-)sequencing</b>
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− | ** What should the elegans reference sequence be?
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− | *** 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.
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− | *** Re-sequencing a standard N2 isolate and make available from CGC.
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− | **** This has been discussed and proposed a number of times, but has never progressed from "That's a really good idea" :(
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− | **** Requires willing lab to prep large number of samples
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− | **** Requires money for new tech seq run
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− | ** Handling 1000s of elegans mutant and wild isolate strain genomes?
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− | *** Representation of non-reference variants of genes/features etc.
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− | ** Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?
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− | * <b>(Re-)distribution of tasks within the consortium</b>
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− | ** Array probe mapping
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− | ** RNAi target identification
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− | ** ''C.elegans'' monthly clone submission
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− | * <b>Visualisation</b>
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− | ** GBrowse: making it -seq friendly
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− | ** Interaction browser: what shall we use?
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− | * <b>website development</b>
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− | ** implications of freeze on current website development - should we make this public?
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− | ** will existing developments be incorporated into new website at start?
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− | ==Thursday 3rd Feb – Millikan Board Room==
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− | === 9:00 - 12:00: Overview, Website / UI ===
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− | * Introduction: Where we are; Hinxton Reorganization - (Paul Sternberg; 15 min)
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− | * Slot for new Hinxton PIs (Paul Kersey and Matt Berriman; 30 mins)
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− | * User interface
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− | ** Site usage; introduction to the new site (Todd; 30 minutes) ([http://prezi.com/sbn2hbidvyry/wormbase-the-website/ Presentation on Prezi.com])
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− | ** Tour of the new website (Abby; 30 minutes)
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− | * Process and pathway curation and display (Karen; 10 minutes)
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− | * Data Integration/Data Mining - WormMart & Future Perspectives (Ruihua; 10 minutes)
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− | ===12:00 – 13.00 Lunch===
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− | ===13:00 – 15:00 Build, Genetic data, Sequence curation and analysis, other nematodes ===
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− | * Build update - Kevin H. (20 mins)
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− | * Genetic data - Mary Ann (presented by Kevin; 20 mins)
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− | * ''C. elegans'' + Tier II Manual curation and projects - Paul D. (20 mins)
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− | * Non-elegans species - an update - Michael P. (20 mins)
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− | * Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
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− | ** microarray and SPELL -Wen C. (5 min)
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− | ===15:00 – 15:30 Break===
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− | ===15:30 - 17:00: Literature Curation===
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− | * Literature curation introducton : Gary Schindelman (update on stats) - 7-10 minutes
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− | * Ontology Annotator
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− | ** Juancarlos Chan - general introduction of OA (15 min)
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− | **Xiaodong Wang - developing interaction OA; BioGRID (5-10 min)
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− | * Picture curation : Daniela Raciti - 10 minutes
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− | * Virtual Worm Overview : Chris Grove - 3 minutes
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− | * Collaboration with other Databases/Projects - automation (ARRA), GO
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− | **journal article processing (GSA markup) Arun, Karen (15 min)
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− | ** Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)
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− | ** Semi-Automated GO Curation - Exporting our Cellular Component Curation Pipeline to other MODs, Progress on Molecular Function Pipeline (Kimberly; 10 minutes)
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− | *WormBook (Jane Mendel, 10 minutes)
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− | ===17:00 - 17:30: General Discussion===
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− | * to be determined during talks
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− | ==Friday 4th Feb – Millikan Board Room==
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− | ===8:30 – 9:00 Advisors breakfast===
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− | ===9:30 – 12:00 Advisors summary report===
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− | ===12:00 – 13:00 Lunch===
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− | ===13:00 – 15:00 Post ABM Discussion===
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− | '''(Advisory Board not required to attend this session)'''
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− | == Arrivals/Departures ==
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− | <b>Arrive</b>
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− | * Hinxton Crew - Pasadena Tuesday afternoon/evening?
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− | * Kimberly - Pasadena, Monday 1/31 evening
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− | * Ranjana - Tuesday, 2/1 evening
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− | <b>Depart</b>
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− | * Hinxton Crew minus Michael - Pasadena Sunday before lunch?
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− | * Michael P. - Pasadena Saturday morning
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− | * Kimberly - Friday, 2/4 evening
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− | * Ranjana - Saturday afternoon
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