Difference between revisions of "WBConfCall 2014.11.13-Agenda and Minutes"

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* Integrated search (2 way WormBase <-> Parasite)
* Integrated search (2 way WormBase <-> Parasite)
* Links on landin pages
* Links on landing pages
* WBBanner links (Species Resources Tools WBParasite)
* WBBanner links (Species Resources Tools WBParasite)
* Parasite on Tool Bar
* Parasite on Tool Bar

Revision as of 13:10, 14 November 2014


Apologies for absence

Mary Ann

Todd will be 15-20mins late


Majority since last Friday resolved or the user is in direct contact with a curator.

Only issue outstanding #3363 - rol-3/srf-2 Typo in ?Interaction object
I'll take care of it. -Karen


Could curators check that their models proposals are included on the WS247 Models wiki page

WS247 Models cycle

Freeze 28th Nov with a view to upload around 20th Dec?

ParaSite findable from wormbase.org

See ticket 3311. What can be achieved quickly and easily?

WormBook chapter on WormBase

How urgent is this? What timeframe should we be working towards?

WS246 release cycle

For the purposes of blog posts etc. it would be good to have a planned www.wormbase.org WS246 intention.

Conference call schedule for rest of year


  • November 13th (today)
  • December 4th
  • December 18th


WS247 Models and Build schedule

5th December Models Freeze 9th January Upload 12th Jan build starts

WormBook Chapters


  • Overview
  • Genome annotation (ncRNAs etc.)
  • Anatomy & Cells - Raymond
  • Gene Expression
    • Gene Function
    • Interaction
  • Disease
  • Comparative genomics and Orthology (? and Parasite)
  • Website
  • Nomenclature
  • Strains
  • Others (PS will send a complete list of proposed chapters)


  • 1/2 our user community at any single point are new/just starting so should adopt a user guide approach/style
  • What data we have
  • How to use our data
  • How we present the data
  • What don't we have or would like to develop
  • 10-20 Pages - don't have to include everything


  • Prepare data/drafts in February
  • Draft chapters can be circulated to a small group of worm researchers as they are ready (PS lab)
  • Submit by April
  • PS Editor + 1 Outside observer (Poss Tim)
  • 1/2 should be reviewed by Worm Meeting
  • Should be a quick turnaround for review.

Things to Consider:

  • Future proofing
    • Try to write to stand test of time
      • Write in a modular approach so that sections can be updated - small changes can be updated in a day
      • Make general statements "As of WS247".

Parasite Integration

Conceptually we would like:

  • Integrated search (2 way WormBase <-> Parasite)
  • Links on landing pages
  • WBBanner links (Species Resources Tools WBParasite)
  • Parasite on Tool Bar
  • Utilising the Species dropdown would be difficult as it would be cluttered, need to think of a cleaner way.
  • Parasite already links back from the gene trees to WBcentral.
  • Parasite will add a WormBase link in the header next to the Downloads.
  • Need to think a bit more about explicit entity linking.

General Questions/Discussion

Q) How many nematode genomes does Parasite have? A) Has 89 genomes (Nematodes/Flatworms) of which ~50 are Nematodes.

D) Caenorhabditis sequencing project Mark Blaxter has a Portal running for his 29 Caenorhabditis project. Seems he wants to control data flow. How can we be involved? There is some discussion on the planned sequencing of these as the resulting genomes might hot be of great quality, would it be better to do smaller numbers but better quality?

D) Users are heading to UCSC for multiple alignment data, what can we do? Michael has started UCSC assembly hub, looking into comparative analysis with Cactus to create data for the hub and could possibly use for www.wormbase? Not entirely sure about WB integration. Tools for beds and wiggle plot files? We need conservation track at minimum.

Parasite is planning multiple alignment views, but not high priority at the moment.

D) Protein aligner in WB is problematic, there are however 2 routes into this data. Parasite has dynamic protein alignments, PS said he will check it out.

Meeting closed after 34mins