2016 Advisory Board Meeting
The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 2016.
- Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
- Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright
- Will fly out on the 2nd of Feb, and return on Sun 7th Feb (cheap flights)
- Arrive 3rd Feb, depart 6th Feb
- Remote workers
- Mary Ann - arrive 2nd Feb (evening), leave 7th Feb (evening)
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.
- How can we work with other MODs on curation strategy?
- 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?
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
- WormBase and human disease
- Linking C. elegans alelles to human pathogenic variants, or variants of unknown significance
- 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
- Gene summaries-legacy manual descriptions, the automatic gene descriptions, and community contributions
- How do we reconcile the different descriptions?
- Community contributions could be to a manual description, to an automated one or could be entirely new
- Which ones do we choose to show on the website? Showing all of them will be messy, and probably will confuse the users more than they will help
- When do we pull the plug on the manual descriptions? Is it worth initiating a project to merge the manual and automatic descriptions
Google drive with useful docs in https://drive.google.com/drive/u/0/folders/0BwFG0nRdT4ZGVjM1REpNT0Q5YXM
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 1 - Automated reading (extraction) - Karen
- 0945-0955 - Automation 2 - Automated writing (synthesis): Automated gene summaries - Ranjana
- 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris
- 1005-1015 - Micropublications - an incentive for community participation - Daniela
- 1015-1025 - LEGO - Kimberly
- 1025-1045 - Discussion (+ specific questions for SAB)
- 1045 - 1100 : BREAK
- 1100 : Genomics
- 1100-1120 - Overview - management and curation of nematode genomic data - Kevin
- 1120-1140 - Curation and analysis of all C. elegans RNASeq gene expression data - Gary
- 1140-1200 - WormBase and parasitic worms - Jane
- 1200-1230 - Discussion (+ specific questions for SAB)
- 1230-1330 : LUNCH
- 1330 : User interface
- 1330-1345 - Website - architecture, structure, usage, outreach - Todd
- 1345-1350 - JBrowse - A new genome browser for WormBase - Todd
- 1350-1400 - Focus on new website features - Sibyl
- 1400-1410 - Visualisation of Ontology annotations (incl WOBr, SObA etc) - Raymond
- 1410-1425 - WormMine - Todd
- 1425-1500 - Discussion (+ specific questions for SAB)
- 1500-1515 : BREAK
- 1515: Infrastructure and interoperability
- 1515-1530 - Overview of current data management strategy and vision for future - Todd / Kevin
- 1530-1545 - Database migration - status and roadmap - Adam
- 1545-1600 - The InterMOD project and cross-MOD interoperability - Todd
- 1600-1630 - Discussion (+ specific questions for SAB)
1630-1645 : BREAK
- 1645-1800: General discussion
- Threat to NIH funding and alternative funding strategies
- Working more closely with other MODs
- How to make WormBase more useful/appealing to biomedical scientists
Fri 5th Feb
- 0800-0900 : Advisors breakfast
- 0900-1130 : Advisors report back to whole group
- 1400-whenever : Project meeting (part two)