Difference between revisions of "2016 Advisory Board Meeting"

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== Organisation of SAB talks ==
 
== Organisation of SAB talks ==
  
Propose organising the agenda into the following cross-site themes:
+
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'''
+
* '''Increasing curation throughput''''
** Current status
+
** Automating curation (Text mining, automated concise descriptions etc) - ??
*** Gene function / literature curation - CALTECH
+
** Community curation  
*** Genome (annotation) curation (gene structures etc) - HINXTON
+
*** Overview and status - Mary Ann
** Scaling up literature curation - CALTECH
+
*** Community phenotype curation and tracking - Chris
*** Increased use of automation (text mining, automated concise descriptions)
+
*** Incentivising contributions - micropublications - Daniela
*** Community curation status and Micropublications
+
** Discussion (+ specific questions for SAB)
**** Community phenotype curation and tracking (Chris)
+
*** How can we work with other MODs on curation strategy?
  
* '''User experience'''
+
* '''User interface'''
** Overview of entry points to WormBase data
+
** Visualisation of complex data
*** Main web-site + FTP site (incl. usage) - OICR
+
*** Ontology annotations (incl WOBr, SObA etc) - Raymond
*** ParaSite - HINXTON
+
*** Quantitative gene expression data - Gary/Sibyl
*** Access to WormBase data via other resources (INSDC, Ensembl, UCSC assembly hub)  - HINXTON
+
** WormMine - Paolo
** Visualisation of complex data - CALTECH
+
** Discussion (+ specific questions for SAB)
*** WOBr, SObA (Raymond)
+
***What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
** Data mining - OICR
+
 
*** WormMine, ParaSite BioMart
+
* '''Parasitic worms'''
** Plans for new tools - ?
+
** Scaling up integration/curation of worm genomics data to parasites - Kevin
*** e.g. enrichment tool, RNASeq querying
+
** WormBase ParaSite - Bruce
** Documentation and outreach strategy - OICR
+
** Discussion (+ specific questions for SAB)
  
 
* '''Infrastructure and interoperability'''
 
* '''Infrastructure and interoperability'''
** Overview of current data management infrastructure - OICR / HINXTON
+
** Database migration : progress and status - Adam
*** Acedb, Ensembl, Postgres, Intermine, BioMart
+
** Interoperability with other MODs (incl InterMod project) - Todd
** Database migration : progress and status - OICR / HINXTON
 
*** Clear summary of project goals
 
*** Progress to date
 
*** Roadmap for next 6-12 months
 
** Interoperability with other MODs - OICR
 
*** InterMod project
 
  
 
* '''General discussion'''
 
* '''General discussion'''
** Strategies to address threat to NIH funding
+
** 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 ==
  
(tentative)
+
* 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
  
* 0900-1200 : Curation : status and plans
+
* 1645: General discussion
* 1300-1500  : User experience
+
** 1645-1715 : Threat to NIH funding and alternative funding models
* 1530-1630  : Infrastructure (incl database migration)
 
* 1630-1800 : General discussion
 
  
 
== 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.

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


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)
  • 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)