Difference between revisions of "WormBase SAB Meeting"

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6:30 – 18:00</b>
 
6:30 – 18:00</b>
  
Put right the World
+
=== Put right the World: Potential Discussion topics ===
  
DISCUSSION TOPICS
+
* Release cycle
    - Release cycle
+
** Implications of less frequent releases
    - Sequence curation manual versus RNA-seq; how do we automate creation of new isoforms
+
** Strategies for "as live" display of certain data types
    - Handling EST-based and fragmented genomes
+
* Gene-structure curation
    - GBrowse: making it -seq friendly
+
** Manual versus automatic-RNASeq-guided (and how we might do the latter)
    - Interaction browser:  what shall we use?
+
** Which genomes should be manually curated?
    - Resequencing a standard N2 isolate
+
** Community annotation of tierIII genomes
    - Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?
+
** Should we invest resources into "semi-automatic" annotation of 3rd party genomes?
    - Minimum requirements for a genome to be allowed into WormBase - submission to EMBL/GenBank, gene prediction?
+
* New species
    - Which genomes should be manually curated?
+
** Minimal requirements for integration into WormBase(
 +
*** Submission to ENA/Genbank? Gene-set?
 +
** Support for "tier IV" (transcriptome-only) genomes
 +
** Support for "in-progress" genome projects (c.f. Ensembl pre-sites)
 +
* (Re-)sequencing
 +
** What should the elegans reference sequence be?
 +
*** Re-sequencing a standard N2 isolate?
 +
** Handling 1000s of elegans mutant and wild isolate strain genomes?
 +
*** Representation of non-reference variants of genes/features etc.
 +
** Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?
 +
* (Re-)distribution of tasks within the consortium
 +
** Array probe mapping
 +
** RNAi target identification
 +
* Visualisation
 +
** GBrowse: making it -seq friendly
 +
** Interaction browser:  what shall we use?
  
 
==Thursday 3rd Feb – Millikan Board Room==
 
==Thursday 3rd Feb – Millikan Board Room==

Revision as of 16:42, 24 January 2011

WormBase Scientific Advisory Board Meeting

Caltechlogo.gif
California Institute of Technology, February 3rd - 4th 2011

Wednesday 2nd Feb – Pre-Meeting (WormBase central)

(AB not required to attend this session)

6:30 – 18:00

Put right the World: Potential Discussion topics

  • Release cycle
    • Implications of less frequent releases
    • Strategies for "as live" display of certain data types
  • Gene-structure curation
    • Manual versus automatic-RNASeq-guided (and how we might do the latter)
    • Which genomes should be manually curated?
    • Community annotation of tierIII genomes
    • Should we invest resources into "semi-automatic" annotation of 3rd party genomes?
  • New species
    • Minimal requirements for integration into WormBase(
      • Submission to ENA/Genbank? Gene-set?
    • Support for "tier IV" (transcriptome-only) genomes
    • Support for "in-progress" genome projects (c.f. Ensembl pre-sites)
  • (Re-)sequencing
    • What should the elegans reference sequence be?
      • Re-sequencing a standard N2 isolate?
    • Handling 1000s of elegans mutant and wild isolate strain genomes?
      • Representation of non-reference variants of genes/features etc.
    • Chip-seq and other large datasets - where should the be stored to maximise usage but cut overhead?
  • (Re-)distribution of tasks within the consortium
    • Array probe mapping
    • RNAi target identification
  • Visualisation
    • GBrowse: making it -seq friendly
    • Interaction browser: what shall we use?

Thursday 3rd Feb – Millikan Board Room

9:00 - 12:00: Overview, Website, UI

  • Introduction: Where we are; Hinxton Reorganization - (Paul Sternberg; 15 min)
  • Slot for new Hinxton PIs (Paul Kersey and Matt Berriman; 30 mins)
  • User interface
    • Site usage; introduction to the new site (Todd; 30 minutes)
    • Tour of the new website (Abby; 30 minutes)
  • Process and pathway curation and display (Karen; 10 minutes)
  • Data Integration/Data Mining - WormMart (Ruihua; 10 minutes)


13:00 – 15:30 Build, Sequence curation and analysis, other nematodes

  • Build, database and related things - (Kevin Howe; 30 mins)
  • C. elegans(+ Tier II) Manual curation and projects? - Paul D. (20 mins)
  • Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
    • microarray and SPELL -Wen C. (5 min)
  • Tier II genome (re)submissions -
  • Other genome analysis -


15:30 - Literature Curation

  • Literature curation introducton : Gary Schindelman (update on stats) - 5 minutes
  • Ontology Annotator
    • Juancarlos Chan - general introduction of OA
    • Xiaodong Wang - developing interaction OA
  • Picture curation : Daniela Raciti - 10 minutes
  • Virtual Worm Overview : Chris Grove - 2 minutes

Possible topics:

  • Gene Function Curation - concise descriptions (update on numbers, curation approach)
  • Collaboration with other Databases/Projects - automation (ARRA), BioGRID, GO
    • GSA Arun/Karen
    • Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)

General Discussion

  • Coordination among sites
  • Quality control
  • Outreach
  • Database migration community annotation

Friday 4th Feb – Millikan Board Room

8:30 – 9:00 Advisors breakfast

9:30 – 12:00 Advisors summary report

12:00 – 13:00 Lunch

13:00 – Discussion

(AB not required to attend this session)

Arrivals/Departures

Arrive

  • Hinxton Crew - Pasadena Tuesday afternoon/evening?


Depart

  • Hinxton Crew minus Michael - Pasadena Sunday before lunch?
  • Michael P. - Pasadena Friday PM?