2013 Advisory Board Meeting

WormBase_Consortium Scientific Advisory Board Meeting

California Institute of Technology, January 27-29, 2013

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)

10:45 - 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)

15:45 - 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

Morgan Library

Tuesday 29th Jan

9:30 – 12:00 Advisors summary report

Also: discussion of License for use. longterm use of Intermine