Difference between revisions of "2016 Advisory Board Meeting"
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== Specific topics for project meeting / working groups == | == Specific topics for project meeting / working groups == | ||
− | * Cross-site communication | + | * '''Cross-site communication''' |
** Unification of documentation and code; what are our standards for documentation? For code? | ** Unification of documentation and code; what are our standards for documentation? For code? | ||
− | * Database migration | + | * '''Database migration''' |
** Specific plans for the next 6-12 months | ** Specific plans for the next 6-12 months | ||
− | |||
− | |||
** extending use to non-Caenorhabiditis sp | ** extending use to non-Caenorhabiditis sp | ||
− | * Enrichment tool | + | * '''How to better integrate WormBase services (i.e. WB and WBPS)''' |
− | ** | + | ** Integrated search - what do we need to do to make this work? |
+ | ** Cross-site tools | ||
+ | *** Enrichment tool | ||
+ | *** Data mining | ||
+ | **** ParaSite has provision to replace BioMart with a system that supports "biologist friendly" queries, e.g. using set operation (a la EuPathDB, PomBase) | ||
+ | **** Is this on the InterMine road map? | ||
+ | **** If not, can we develop something that can be used in both WB and WBPS that complements (rather than competes with) WormMine? | ||
+ | * '''Texpresso for parasitic worms''' | ||
+ | ** Discussions already started on this | ||
+ | |||
+ | |||
= Agenda (preliminary) = | = Agenda (preliminary) = |
Revision as of 14:24, 8 January 2016
The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 2016.
Contents
Logistics
Attending
- Hinxton
- Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
- OICR
- Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright, Paulo Nuin
Travel
- Hinxton
- Will fly out on the 2nd of Feb, and return on Sun 7th Feb (cheap flights)
- OICR
- Arrive 3rd Feb, depart 6th Feb
- Remote workers
- Mary Ann - arrive 2nd Feb (evening), leave 7th Feb (evening)
Advisors
- Jason Stajich
- Mike Cherry
- Brian Oliver
- Oliver Hobert
- Monte Westerfield
- Robin Gasser (possible)
Discussion topics
Organisation of SAB talks
Agenda for the SAB itself will be organised into 4 main sections. Each section will have a short overview/scene-setting talk, followed by selected specfic talks. Each section will end with a time-tabled open discussion, which we should use to discuss strategy in that area, and put any specfic questions we have to the advisory board. Please add suggested questions/discussion topics for each section below.
- Curation
- How can we work with other MODs on curation strategy?
- Genomics
- How should we prioritise species for curation effort?
- Would a community curation system for gene models be useful for nematodes?
- Integration between WormBase and WB ParaSite - to what extent is this required?
- User interface
- How best to measure the utility of WormBase (and similar resources)?
- What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
- Infrastructure and interoperability
- How important is it that our infrastructure solution is reusable by other MODs (or genomics data management projects)
- Is the amount of effort we invest in maintaining/extending wormMine typical for other *Mine deployments?
- Is use of non-open-source software for core data management an acceptable risk?
Other potential talks (if we want/need to fill time)
- Genome annotation curation - status and plans - Paul Davis
- Documentation and outreach strategy - Todd
- Integration and curation of the new B. malayi genome assembly v4 - Michael
Specific topics for project meeting / working groups
- Cross-site communication
- Unification of documentation and code; what are our standards for documentation? For code?
- Database migration
- Specific plans for the next 6-12 months
- extending use to non-Caenorhabiditis sp
- How to better integrate WormBase services (i.e. WB and WBPS)
- Integrated search - what do we need to do to make this work?
- Cross-site tools
- Enrichment tool
- Data mining
- ParaSite has provision to replace BioMart with a system that supports "biologist friendly" queries, e.g. using set operation (a la EuPathDB, PomBase)
- Is this on the InterMine road map?
- If not, can we develop something that can be used in both WB and WBPS that complements (rather than competes with) WormMine?
- Texpresso for parasitic worms
- Discussions already started on this
Agenda (preliminary)
Wed 3rd Feb
- 1400 : Project meeting (part one)
Thu 4th Feb
- 0915-0930 - Introduction - Paul Sternberg
- 0930 : Literature curation
- 0930-0935 - Overview - status and priorities - Chris
- 0935-0945 - Automation - doing more with less (SVMs and Automated gene descriptions) - Ranjana
- 0945-0955 - Community curation - overview, status, tracking - Mary Ann & Chris
- 0955-1005 - Micropublications - an incentive for community participation - Daniela
- 1005-1015 - LEGO - Kimberly
- 1015-1045 - Discussion (+ specific questions for SAB)
- 1045 - 1100 : BREAK
- 1100 : Genomics
- 1100-1125 - Integration and curation of hundreds of nematode genomes - Kevin
- 1125-1145 - Curation and analysis of all nematode RNASeq gene expression data - Gary
- 1145-1210 - WormBase ParaSite - Bruce
- 1210-1245 - Discussion (+ specific questions for SAB)
- 1245-1345 : LUNCH
- 1345 : User interface
- 1345-1410 - WormBase web-site - usage, outreach etc - Todd
- 1410-1420 - JBrowse - A new genome browser for WormBase
- 1420-1430 - Visualisation of Ontology annotations (incl WOBr, SObA etc) - Raymond
- 1430-1445 - WormMine - Paulo
- 1445-1515 - Discussion (+ specific questions for SAB)
- 1510-1530 : BREAK
- 1530: Infrastructure and interoperability
- 1530-1545 - Overview of current data management strategy and vision for future - Todd / Kevin
- 1545-1605 - Database migration - status and roadmap - Adam
- 1605-1615 - The InterMOD project and cross-MOD interoperability - Todd
- 1615-1645 - Discussion (+ specific questions for SAB)
1645-1700 : BREAK
- 1700: General discussion
- Threat to NIH funding and alternative funding strategies
- Working more closely with other MODs
Fri 5th Feb
- 0800-0900 : Advisors breakfast
- 0900-1130 : Advisors report back to whole group
- 1400-whenever : Project meeting (part two)