2016 Advisory Board Meeting
The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 2016.
- Caltech Map: Media:Caltech Map SAB 2016.pdf
- Instructions for connecting to Network: Media:Wireless Instructions.pdf
- 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)
- Jason Stajich
- Mike Cherry--not present
- Brian Oliver
- Oliver Hobert
- Monte Westerfield
- Raffi Aroian
- Anne Villeneuve
- Andrew Chisholm, WormBoard
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?
- Are our priorities for curation appropriate?
- How can we best make use of LEGO annotation?
- C. elegans
- Should we update the reference genome with data from Li et al?
- What is the status of the initiative to select (and sequence) a new reference strain?
- Should we curate gene models in key strain genomes (e.g. Hawaiian)?
- A graph genome for C. elegans?
- Is curation/processing/display of all RNASeq data sets for C. elegans valuable? Sustainable?
- Other species
- What criteria should be used to assess whether a genome is elevated to "core" status?
- Is special treatment of C. briggsae, C. remanei, C. brenneri and C. japonica still justified in light of the Caenorhabditis genome project?
- Would a community curation system for gene models be successful for nematodes?
- Where to focus curation effort for other nematodes?
- Integration between WormBase and WB ParaSite - to what extent is this required?
- C. elegans
- 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
- What about a disease portal? Could be as simple as having a separate tab, this serves to increase visibility
- Increasing number of papers on therapeutics for disease (drugs, small molecules, herbals)
- Increasing number of papers on disease exacerbating metals and compounds (falls into two broad areas-disease and toxicity)
- 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, one too many: legacy manual descriptions, the automatic gene descriptions, and community contributions
- A plan to phase out the un-maintainable manual descriptions: Start with the oldest (by last_updated date) descriptions
- Currently community contributions could be to a manual description, to an automated one or could be entirely new
- With the automated descriptions being amenable to updates and the addition of new data (as and when they get curated in WB), should we even solicit community contributions?
- How do we merge the community contributions and the automated descriptions? Should we display them as one or separate them?
Google drive with useful docs in https://drive.google.com/drive/u/0/folders/0BwFG0nRdT4ZGVjM1REpNT0Q5YXM
Wed 3rd Feb
- 1400 : Project meeting (part one). Morgan Library (Kerckhoff 2nd fl)
Thu 4th Feb
Keck Conference Center (Building 127, Room 155, Head towards the Broad cafe, past the gene pool)
- 0900-0915 - Arrivals and discussion
- 0915-0930 - Introduction - Paul Sternberg
- 0930 : Literature curation
- 0930-0935 - Overview - status and priorities - Chris Grove
- 0935-0945 - Automated identification of data - Karen Yook
- 0945-0955 - Automated writing of gene summaries - Ranjana Kishore
- 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris
- 1005-1015 - Micropublications - an incentive for community participation - Daniela Raciti
- 1015-1025 - LEGO - Kimberly Van Auken
- 1025-1045 - Discussion (+ specific questions for SAB)
- 1045 - 1100 : BREAK
- 1100 : Genomics
- 1100-1120 - Overview - genomics at WormBase - Kevin
- 1120-1140 - Curation and analysis of all 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) - 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 - 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
Millikan Library Board room
- 0800-0900 : Advisors breakfast
- 0900-1130 : Advisors report back to whole group
- 1400-whenever : Project meeting (part two)