WBConfCall 2013.09.19-Agenda and Minutes

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1. Models summary/sign-off for WS240

2. ORCID for WBPerson ?

3. Natural variation wish-list reported by Marie-Anne Felix

  • For each polymorphism, please show (i) strains that carry that variation and (ii) strains that are confirmed to have the reference allele at that position
    • (i) is done, (ii) is a lot harder, because submitters do not distinguish between reference and no-data for a given position
    • related problem: what do we do when change the reference genome in the location of a SNP?
  • How do we propose to handle other classes of variation (transposon insertions, copy-number variants, genomic rearrangements)?
    • I thought we already did, but only limited data of this kind has been submitted for wild isolates
  • Collapsing of redundant variations - it is important that the source/attribution for the allele in each strain is shown
    • WS239 contains all attribution data, although we will be making it a bit easier to access for WS240. Not currently being displayed though
  • Please show nucleotide position of the feature, rather than nucleotide position of the surrounding context of the feature
    • I would like to see this too!
  • Please promote the putative consequence(s) of the SNP to the Overview widget of the Variation page, and make putative consequence a queryable attribute in WormMine
  • Please give us an all-singing, all-dancing sequence variation browser
    • Web-team to comment

4. WormMine Update

5. WormBase development environment for Caltech. (local installation / access to OICR dev / Amazon AMI)

Help Desk issues

Dealing with Natural Variation - from Marie-Anne Felix. (Mary Ann/Kev) https://github.com/WormBase/website/issues/1735 Promoted to main agenda above
Including a new method - Dan Dickinson https://github.com/WormBase/website/issues/1762 made a website for sharing protocols from our lab: http://wormcas9hr.weebly.com/. I wanted to ask if you'd consider putting a link to this page somewhere on the Wormbase website. created methods widget on resources page, it will go there.
Gbrowse error https://github.com/WormBase/website/issues/1722 Joachim, after next release.
Add balancer location to tracks https://github.com/WormBase/website/issues/1717 Todd need to look up what we need, add it to gff3, then display it
extra zero in WB grant number https://github.com/WormBase/website/issues/1779 Verify? paul will look up grant number, then webteam will fix it. Paul: grant number is u41hg002223. will include full grant number.
old release gateway timeout https://github.com/WormBase/website/issues/1761 Todd, links to old releases return gateway timeout low priority, Todd looking at frozen releases, still working on it
How Do I ...?: see the tiling arrays? https://github.com/WormBase/website/issues/1685 looks resolved, close? poster is asking about his own data in WB. Kevin: this data not in DB, hinxton doesn't make wiggle tracks. recreate track from scratch or reactivate old track? email poster chris link about the data, see what he wants. Todd will contact him and handle the issue.
n765 is lin-15AB, not lin-15B. https://github.com/WormBase/website/issues/1471 Karen. issue is not resolved. This issue needs input from the team - specifically, discussion about
1. how to annotate alleles that affect more than one gene, or do not lie within the defined gene sequence boundaries
2. what to display on the lin-15 page.
mary-ann, karen, paul D. will handle this
BLAST not working for alignment to WS235 https://github.com/WormBase/website/issues/1443 Joachim. issue resolved? issue not resolved, Joachim will work on it
wormbase-compara version is missing https://github.com/WormBase/website/issues/1231 Michael P. issue resolved? no Michael will handle it
BED file upload size limit? https://github.com/WormBase/website/issues/673 Todd. issue resolved? we're looking into other genome browsers as per grant. relates to that. issue unresolved for now
Implement region search https://github.com/WormBase/website/issues/507 feature can be added to WormMine for intervals by raw coordinate only, not by intervals defined sequence feature name JD will implement intermine solution, discussion on specific types mapped will continue from there.


1. models for 240 haven't changed, mostly tag additions or tag replacements

2. if person provides their id we can add it. have to use DB tag or create new tag. we dont have orcid tag in db. db tag would.

timetable on receiving funding? shouldn't take that long.