WormBase SAB Meeting
Tentative schedule for WormBase Advisory board meeting 2014 EBI, Hinxton, UK
Sunday 5th October PM: Consortium meeting, EBI (advisors not present) Monday 6th October: whole-group advisory board meeting (talks and discussion), EBI Tuesday 7th October. AM: advisors report back to either whole group; PM: 1-2, post-meeting discussion of action items emanating from the meeting.
Logistics: acccomodation (EBI housing??) SAB: arrive Sunday evening, leave Tuesday afternoon Staff: arrive Sat evening (or Sunday morning), leave Tuesday afternoon/evening
BELOW is last year and should be moved to another page
WormBase_Consortium Scientific Advisory Board Meeting
- 1 Advisors list
- 2 Questions to address the Advisory Board
- 3 Sunday 27th Jan – Pre-Meeting (WormBase central)
- 4 Monday 28th Jan
- 4.1 9:00 - 9:15 Overview
- 4.2 9:15 - 10:30 Website / User interface
- 4.3 10:30 - 10:45 BREAK
- 4.4 10:45 - 12:15 Sequence analysis and curation
- 4.5 12:15 - 13:30 LUNCH
- 4.6 13:30 - 15:30 Literature curation
- 4.7 15:30 - 15:45 BREAK
- 4.8 15:45 - 17:30 Curation Continued and Other topics
- 4.9 17:30 - Drinks and Dinner
- 5 Tuesday 29th Jan
- 6 Prior Meetings
Questions to address the Advisory Board
- How can we best handle the multiple nematode genomes, display the data and provide analytical tools to our users?
- How can we handle natural variation in C. elegans and other species?
- How can we display and analyze transcriptional regulatory networks?
- How can we best capture and display biological pathways?
- How can we best capture community annotation or help from the community?
- How do we make WormBase accessible and useful to human geneticists?
- How should we prioritize RNAi versus other gene function curation?
- How important are daily/weekly updates? How best to implement?
- How should we make use of microarray/RNA-seq data?
Sunday 27th Jan – Pre-Meeting (WormBase central)
(Advisory Board not required to attend this session) Kerckhoff Room 101 : 1:30pm
- WormBase ParaSite
- Licence / formal data release policy
- Incremental updates
- Operational issues
- Revive GFF3 production/testing
- Representation of multiple assemblies for a single species (on web-site and FTP site)
- Data freezes
- Frequency, extent, format
- Web-site wish list(s)
- Mechanism to stage/review changes to static content without immediately publishing it to live site
- variation tracks
- New comparative genomics views (multiple alignments, gene trees)
- normalizing IDs, globally to allow intermine compatibility
Monday 28th Jan
9:00 - 9:15 Overview
- 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)
- The 50 Helminth Genome Project (Matt B; 10 mins)
- Transcriptomics data in WormBase
- RNASeq alignment and annotation pipeline (Gary W; 10 mins)
- SPELL (Wen; 10 mins)
- Sequence curation - current status and future plans (Paul; 15 mins)
- Annotation of Brugia malayi - a pilot study for future parasitologist community collaborations (Michael; 15 mins)
12:15 - 13:30 LUNCH
Morgan Library (second floor of Kerckhoff)
13:30 - 15:30 Literature curation
- Literature curation workflow and tools (Chris, 30)
- Interactions (15)
- Transcriptional Networks: Gene expression and regulation: Transcriptional Networks (Daniela 10; Xioadong 30)
- Human Relevance - Disease and Drugs (Ranjana,10)
15:30 - 15:45 BREAK
15:45 - 17:30 Curation Continued and Other topics
- GO and LEGO (20)
- Pathways [Karen, 20]
- Discussion of Integrated Phenotype Curation (alleles, RNAi, transgenes, interactions, GO, cell function (10)
- Biological data for other species
- Concise descriptions [Kimberly, Ranjana; 15]
- Sequence Curation; Priorities for WormBase; Community Annotation; etc. (20)
- Plans for retirement of the Acedb (Kevin/Todd; 15 mins)
17:30 - Drinks and Dinner
Tuesday 29th Jan
8:30 – 9:00 Advisors breakfast
9:30 – 12:00 Advisors summary report
Also: discussion of License for use. longterm use of Intermine