|
|
(105 intermediate revisions by 11 users not shown) |
Line 1: |
Line 1: |
− | <center><b>
| |
− | <font size="5" color="Blue">[[WormBase_Consortium]] Scientific Advisory Board Meeting
| |
| | | |
− | [[File:Caltechlogo.gif|frame|none]]California Institute of Technology, February 3rd - 4th 2011 | + | = Meeting list = |
− | </font>
| + | [[2018_Advisory_Board_Meeting | 2018 SAB Meeting]] |
− | </b></center>
| |
− | __TOC__
| |
| | | |
− | ===[[WormBase_Consortium#Scientific_Advisory_Board |Advisors list]]===
| + | [[2016_Advisory_Board_Meeting | 2016 SAB Meeting]] |
| | | |
− | ==Wednesday 2nd Feb – Pre-Meeting (WormBase central)==
| + | [[2014_Advisory_Board_Meeting | 2014 SAB Meeting]] |
− | '''(Advisory Board not required to attend this session)'''
| |
| | | |
− | <b>9:00 - 9:15 </b>delegates arrive
| + | [[2013_Advisory_Board_Meeting | 2013 SAB Meeting]] |
| | | |
− | <b>9:15 - 9:30 </b>pre-pre-meeting coffee
| + | [[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?
| |
− | ** 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 (Ruihua; 10 minutes)
| |
− | | |
− | ===12:00 – 13.00 Lunch===
| |
− | | |
− | ===13:00 – 15:00 Build, Sequence curation and analysis, other nematodes===
| |
− | | |
− | * Build update - Kevin H. (20 mins)
| |
− | * ''C. elegans'' (+ Tier II) Manual curation and projects? - Paul D. (20 mins)
| |
− | * Genetic data - Mary Ann (presented by a Hinxton surrograte; 15 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 (5-10 min)
| |
− | | |
− | * Picture curation : Daniela Raciti - 10 minutes
| |
− | * Virtual Worm Overview : Chris Grove - 3 minutes
| |
− | | |
− | * Gene Function Curation - concise descriptions (update on numbers, curation approach) - not sure if this is necessary if Gary presents the overall numbers --kmv
| |
− | | |
− | * Collaboration with other Databases/Projects - automation (ARRA), GO
| |
− | **GSA Arun/Karen
| |
− | ** 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; 5-10 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
| |
− | | |
− | | |
− | <b>Depart</b>
| |
− | | |
− | * Hinxton Crew minus Michael - Pasadena Sunday before lunch?
| |
− | * Michael P. - Pasadena Friday?
| |
− | * Kimberly - Friday, 2/4 evening
| |