Difference between revisions of "2016 Advisory Board Meeting"
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* [http://irp.nih.gov/pi/brian-oliver Brian Oliver] | * [http://irp.nih.gov/pi/brian-oliver Brian Oliver] | ||
* [http://hobertlab.org/ Oliver Hobert] | * [http://hobertlab.org/ Oliver Hobert] | ||
− | * Monte Westerfield | + | * [http://www.neuro.uoregon.edu/westerf/lab.html Monte Westerfield] |
* Robin Gasser (possible) | * Robin Gasser (possible) | ||
Revision as of 16:55, 7 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
Proposal: Prepare a short report for the advisors containing project status. For the SAB talks, restrict to a small(er) number on specific topics that are new, or where we want advice.
- Curation
- Overview - status and priorities - Chris
- Automating curation (Text mining, automated concise descriptions etc) - ? + Ranjana
- Community curation
- Overview and status - Mary Ann
- Community phenotype curation and tracking - Chris
- Incentivising contributions - micropublications - Daniela
- Discussion (+ specific questions for SAB)
- How can we work with other MODs on curation strategy?
- User interface
- Visualisation of complex data
- Ontology annotations (incl WOBr, SObA etc) - Raymond
- Quantitative gene expression data - Gary/Sibyl
- WormMine - Paolo
- Discussion (+ specific questions for SAB)
- What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
- Visualisation of complex data
- Parasitic worms
- Scaling up integration/curation of worm genomics data to parasites - Kevin
- WormBase ParaSite - Bruce
- Discussion (+ specific questions for SAB)
- Infrastructure and interoperability
- Overview of current data management infrastructure and vision for future - Todd / Kevin
- Database migration : progress and status - Adam
- Interoperability with other MODs (incl InterMod project) - Todd
- General discussion
- How best to measure the utility of WormBase
- Threat to NIH funding and alternative funding models
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
- WormBase + WBParaSite integration
- Textpresso
- extending use to non-Caenorhabiditis sp
- Enrichment tool
- how to implement for both WormBase central and ParaSite
Agenda (preliminary)
Wed 3rd Feb
- 1400 : Project meeting (part one)
Thu 4th Feb
- 0915-0930 - Introduction - Paul Sternberg
- 0930 : Curation
- 0930-0945 - Overview - status and priorities - Chris
- 0945-0955 - Automating curation - doing more with less: SVMs and Automated gene descriptions - Ranjana
- 0955-1005 - Community curation - overview and status - Mary Ann
- 1005-1015 - Community phenotype curation and tracking - Chris
- 1015-1025 - Incentivising contributions - micropublications - Daniela
- 1025-1045 - Discussion (+ specific questions for SAB)
- 1045 - 1100 : BREAK
- 1100 : Parasitic worms
- 1100-1120 - Scaling up integration/curation of worm genomics data to parasites - Kevin
- 1120-1145 - WormBase ParaSite - Bruce
- 1145-1215 - Discussion (+ specific questions for SAB)
- 1200-1330 : LUNCH
- 1330 : User interface
- 1330-1340 - Visualising Ontology annotations (incl WOBr, SObA etc) - Raymond
- 1345-1405 - Analysis and visualisation of quantitative gene expression data - Gary
- 1405-1430 - WormMine - Paolo
- 1430-1500 - Discussion (+ specific questions for SAB)
- What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
- 1500-1515 : BREAK
- 1515: Infrastructure and interoperability
- 1515-1530 - Overview of current data management strategy and vision for future - Todd / Kevin
- 1530-1550 - Database migration : status and roadmap - Adam
- 1550-1605 - InterMod project and cross-MOD interoperability - Todd
- 1605-1630 - Discussion (+ specific questions for SAB)
1630-1645 : BREAK
- 1645: General discussion
- 1645-1715 : What are the best ways to measure how important/useful WormBase is?
- 1715-1745 : Threat to NIH funding and alternative funding models
Fri 5th Feb
- 0800-0900 : Advisors breakfast
- 0900-1130 : Advisors report back to whole group
- 1400-whenever : Project meeting (part two)