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, January 27-29, 2013
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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]]
==Sunday 27th Jan – Pre-Meeting (WormBase central)==
 
'''(Advisory Board not required to attend this session)'''
 
  
* Revive GFF3 production/testing
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[[2014_Advisory_Board_Meeting | 2014 SAB Meeting]]
* Representation of multiple assemblies for a single species (on web-site and FTP site)
 
* Mechanism to stage/review changes to static content without immediately publishing it to live site
 
* Future web-site features
 
** Incremental updates
 
** Data that we produce that cannot currently be viewed on web-site
 
*** Multiple and pairwise genomic alignments
 
*** Nematode gene trees
 
  
==Monday 28th Jan ==
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[[2013_Advisory_Board_Meeting | 2013 SAB Meeting]]
  
=== 9:00 - 9:15 Overview ===
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[[2011_Advisory_Board_Meeting | 2011 SAB Meeting]]
 
 
* Introduction: Where we are, grant status, etc - (Paul Sternberg; 15 min)
 
 
 
=== 9:15 - 10:30 Website / User interface ===
 
 
 
* Site introduction; usage; web team accomplishments; objectives and milestones. (Todd; 20 minutes)
 
* Tour of the new website (Abby; 20 minutes)   
 
* Intermine introduction, status, and goals (JD; 15 minutes)
 
 
 
=== 10:30 - 10:45 BREAK ===
 
 
 
=== 10:45 - 12:15 Sequence analysis and curation ===
 
 
 
* Coping with the deluge of nematode sequence data (Kevin; 20 mins)
 
* C. elegans sequence curation - current status and future plans (Paul; 15 mins)
 
* Transcriptomics data in WormBase
 
** RNASeq alignment and annotation pipeline (Gary W; 10 mins)
 
** SPELL (Wen; 10 mins)
 
* Annotation of Brugia malayi - a pilot study for future parasitologist community collaborations (Michael; 15-20 mins)
 
 
 
=== 12:15 - 13:30 LUNCH ===
 
 
 
===  13:30 - 16:15 Literature curation ===
 
 
 
* Literature curation workflow and tools (50)
 
* Towards Integrated Phenotype Curation (alleles, RNAi, transgenes, interactions, GO  (30)
 
* Gene expression and regulation: Transcriptional Networks (Xioadong, Daniela)
 
* Interactions (20)
 
* GO (20)
 
* Cell Function (10)
 
* Processes and pathways (20)
 
* Transcriptional Networks
 
* Human Relevance - Orthologies, Disease and Drugs
 
 
 
=== 16:15 - 16:30 BREAK ===
 
 
 
=== 16:30 - 17:30 Other topics ===
 
 
 
* Revisiting tools with respect to Community Annotation (40)
 
** Pathways [Karen]
 
** Concise descriptions [Kimberly, Ranjana]
 
** Gene models (Kevin; 5 mins)
 
* Plans for retirement of the Acedb (Kevin/Todd; 15 mins)
 
 
 
== Tuesday 29th Jan ==
 
 
 
===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===
 
 
 
 
 
= 2011 schedule =
 
 
 
==Wednesday 2nd Feb – Pre-Meeting (WormBase central)==
 
'''(Advisory Board not required to attend this session)'''
 
 
 
<b>9:00 - 9:15 </b>delegates arrive
 
 
 
<b>9:15 - 9:30 </b>pre-pre-meeting coffee
 
 
 
<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) ([http://prezi.com/sbn2hbidvyry/wormbase-the-website/ Presentation on Prezi.com])
 
** 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. (20 mins)
 
* Genetic data - Mary Ann (presented by Kevin; 20 mins)
 
* ''C. elegans'' + Tier II Manual curation and projects - Paul D. (20 mins)
 
* Non-elegans species - an update - Michael P. (20 mins)
 
* Large scale datasets (curation/modENCODE) - Gary W. (30 mins)
 
** microarray and SPELL -Wen C. (5 min)
 
 
 
===15:00 – 15:30 Break===
 
 
 
===15:30 - 17:00:  Literature Curation===
 
* Literature curation introducton : Gary Schindelman (update on stats) - 7-10 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