Difference between revisions of "2016 Advisory Board Meeting"
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== Organisation of SAB talks == | == 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. | |
− | * ''' | + | * '''Increasing curation throughput'''' |
− | ** | + | ** Automating curation (Text mining, automated concise descriptions etc) - ?? |
− | + | ** Community curation | |
− | + | *** Overview and status - Mary Ann | |
− | ** | + | *** Community phenotype curation and tracking - Chris |
− | *** | + | *** Incentivising contributions - micropublications - Daniela |
− | *** Community curation | + | ** Discussion (+ specific questions for SAB) |
− | **** | + | *** How can we work with other MODs on curation strategy? |
− | * '''User | + | * '''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) |
− | * | + | |
− | + | * '''Parasitic worms''' | |
− | ** | + | ** Scaling up integration/curation of worm genomics data to parasites - Kevin |
− | + | ** WormBase ParaSite - Bruce | |
− | ** | + | ** Discussion (+ specific questions for SAB) |
* '''Infrastructure and interoperability''' | * '''Infrastructure and interoperability''' | ||
− | + | ** Database migration : progress and status - Adam | |
− | + | ** Interoperability with other MODs (incl InterMod project) - Todd | |
− | ** Database migration : progress and status - | ||
− | |||
− | |||
− | |||
− | ** Interoperability with other MODs | ||
− | |||
* '''General discussion''' | * '''General discussion''' | ||
− | ** | + | ** Threat to NIH funding and alternative funding models |
+ | |||
+ | Other potential talks (if we want/need to fill time) | ||
+ | |||
+ | * Curation | ||
+ | ** Genome annotation curation - status and plans - Paul Davids | ||
+ | * User interface | ||
+ | ** Documentation and outreach strategy - Todd | ||
+ | * Parasitic worms | ||
+ | ** Integration and curation of the new B. malayi genome assembly v4 - Michael | ||
+ | * Infrastructure and interoperability | ||
+ | * Overview of current data management infrastructure - Kevin | ||
+ | |||
== Specific topics for project meeting / working groups == | == Specific topics for project meeting / working groups == | ||
Line 91: | Line 97: | ||
== Thu 4th Feb == | == Thu 4th Feb == | ||
− | ( | + | * 0915-0930 - Introduction - Paul Sternberg |
+ | * 0930 : Curation | ||
+ | ** 0930-0945 : Automating curation (Text mining, automated concise descriptions etc) - ?? | ||
+ | ** 0945-0955 : Community curation - overview and status - Mary Ann | ||
+ | ** 0955-1005 : Community phenotype curation and tracking - Chris | ||
+ | ** 1005-1015 : Incentivising contributions - micropublications - Daniela | ||
+ | ** 1015-1045: 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 | ||
+ | ** 1515-1535 - Database migration : status and roadmap - Adam | ||
+ | ** 1535-1600 - InterMod project and cross-MOD interoperability - Todd | ||
+ | ** 1600-1630 - Discussion | ||
+ | |||
+ | 1630-1645 : BREAK | ||
− | * | + | * 1645: General discussion |
− | * | + | ** 1645-1715 : Threat to NIH funding and alternative funding models |
− | * | ||
− | |||
== Fri 5th Feb == | == Fri 5th Feb == |
Revision as of 15:49, 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 (possible)
- 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.
- Increasing curation throughput'
- Automating curation (Text mining, automated concise descriptions etc) - ??
- 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
- Database migration : progress and status - Adam
- Interoperability with other MODs (incl InterMod project) - Todd
- General discussion
- Threat to NIH funding and alternative funding models
Other potential talks (if we want/need to fill time)
- Curation
- Genome annotation curation - status and plans - Paul Davids
- User interface
- Documentation and outreach strategy - Todd
- Parasitic worms
- Integration and curation of the new B. malayi genome assembly v4 - Michael
- Infrastructure and interoperability
- Overview of current data management infrastructure - Kevin
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 : Automating curation (Text mining, automated concise descriptions etc) - ??
- 0945-0955 : Community curation - overview and status - Mary Ann
- 0955-1005 : Community phenotype curation and tracking - Chris
- 1005-1015 : Incentivising contributions - micropublications - Daniela
- 1015-1045: 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
- 1515-1535 - Database migration : status and roadmap - Adam
- 1535-1600 - InterMod project and cross-MOD interoperability - Todd
- 1600-1630 - Discussion
1630-1645 : BREAK
- 1645: General discussion
- 1645-1715 : 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)