Difference between revisions of "WormBase SAB Meeting"

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<font size="5" color="Blue">[[WormBase_Consortium]] Scientific Advisory Board Meeting
 
  
[[File:Caltechlogo.gif|frame|none]]California Institute of Technology, February 3rd - 4th 2011
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= Meeting list =
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[[2018_Advisory_Board_Meeting | 2018 SAB Meeting]]
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__TOC__
 
  
===[[WormBase_Consortium#Scientific_Advisory_Board |Advisors list]]===
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[[2016_Advisory_Board_Meeting | 2016 SAB Meeting]]
  
==Wednesday 2nd Feb – Pre-Meeting (WormBase central)==
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[[2014_Advisory_Board_Meeting | 2014 SAB Meeting]]
'''(Advisory Board not required to attend this session)'''
 
  
<b>9:00 - 9:15 </b>delegates arrive
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[[2013_Advisory_Board_Meeting | 2013 SAB Meeting]]
  
<b>9:15 - 9:30 </b>pre-pre-meeting coffee
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[[2011_Advisory_Board_Meeting | 2011 SAB Meeting]]
 
 
<b>9:30 – 18:00</b> Put right the World
 
 
 
Potential Discussion topics
 
<b>
 
* Release cycle
 
</b>
 
** Implications of less frequent releases
 
** Strategies for "as live" display of certain data types
 
<b>
 
* Gene-structure curation
 
</b>
 
** Manual versus automatic-RNASeq-guided (and how we might do the latter)
 
** Which genomes should be manually curated?
 
** Community annotation of tier III genomes
 
** Should we invest resources into "semi-automatic" annotation of 3rd party genomes?
 
<b>
 
* New species
 
</b>
 
** Minimal requirements for integration into WormBase
 
*** Submission to ENA/Genbank? Gene-set?
 
*** Ownership of genome assemblies? Tier IIs required to be owned by Wormbase for re-submission
 
** Support for "tier IV" (transcriptome-only) / "tier V" (genome-only) worms
 
** Support for "in-progress" genome projects (See also [http://pre.ensembl.org/index.html Ensembl pre-sites])
 
<b>
 
* (Re-)sequencing
 
</b>
 
** What should the elegans reference sequence be?
 
*** We have RNASeq evidence from at least four labs for about 500 to 1000 genomic errors in the reference sequence compared to 'their' N2. However each lab has a different set of errors.
 
*** Re-sequencing a standard N2 isolate and make available from CGC.
 
**** This has been discussed and proposed a number of times, but has never progressed from "That's a really good idea" :(
 
**** Requires willing lab to prep large number of samples
 
**** Requires money for new tech seq run
 
** 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?
 
<b>
 
* (Re-)distribution of tasks within the consortium
 
</b>
 
** Array probe mapping
 
** RNAi target identification
 
** ''C.elegans'' monthly clone submission
 
<b>
 
* Visualisation
 
</b>
 
** GBrowse: making it -seq friendly
 
** Interaction browser:  what shall we use?
 
<b>
 
* website development
 
</b>
 
** implications of freeze on current website development - should we make this public?
 
** will existing developments be incorporated into new website at start?
 
 
 
==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 & Future Perspectives (Ruihua; 10 minutes)
 
 
 
===12:00 – 13.00 Lunch===
 
 
 
===13:00 – 15:00 Build, Genetic data, Sequence curation and analysis, other nematodes ===
 
 
 
* Build update - Kevin H. (15 mins)
 
* Genetic data - Mary Ann (presented by Kevin; 15 mins)
 
* ''C. elegans'' (+ Tier II) Manual curation and projects? - Paul D. (20 mins)
 
* Non-elegans species - an update - Michael P. (15 mins)
 
* Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
 
** microarray and SPELL -Wen C. (5 min)
 
* Tier II genome (re)submissions
 
 
 
===15:00 – 15:30 Break===
 
 
 
===15:30 - 17:00:  Literature Curation===
 
* Literature curation introducton : Gary Schindelman (update on stats) - 5-7 minutes
 
 
 
* Ontology Annotator
 
** Juancarlos Chan - general introduction of OA  (15 min)
 
**Xiaodong Wang - developing interaction OA; BioGRID  (5-10 min)
 
 
 
* Picture curation : Daniela Raciti - 10 minutes
 
* Virtual Worm Overview : Chris Grove - 3 minutes
 
 
 
* Collaboration with other Databases/Projects - automation (ARRA), GO
 
**journal article processing (GSA markup) Arun, Karen (15 min)
 
** Automatic Triage - Using Support Vector Machine (SVM) (Ruihua; 10 minutes)
 
** Semi-Automated GO Curation - Exporting our Cellular Component Curation Pipeline to other MODs, Progress on Molecular Function Pipeline (Kimberly; 10 minutes)
 
 
 
*WormBook (Jane Mendel, 10 minutes)
 
 
 
===17:00 - 17:30:  General Discussion===
 
* to be determined during talks
 
 
 
==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 – 15:00 Post ABM Discussion===
 
 
 
'''(Advisory Board not required to attend this session)'''
 
 
 
== Arrivals/Departures ==
 
 
 
<b>Arrive</b>
 
 
 
* Hinxton Crew - Pasadena Tuesday afternoon/evening?
 
* Kimberly - Pasadena, Monday 1/31 evening
 
* Ranjana  - Tuesday, 2/1 evening
 
 
 
<b>Depart</b>
 
 
 
* Hinxton Crew minus Michael - Pasadena Sunday before lunch?
 
* Michael P. - Pasadena Saturday morning
 
* Kimberly - Friday, 2/4 evening
 
* Ranjana  - Saturday afternoon
 

Latest revision as of 12:39, 7 June 2018