Difference between revisions of "WBConfCall 2013.09.19-Agenda and Minutes"

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| https://github.com/WormBase/website/issues/1443
| https://github.com/WormBase/website/issues/1443
| Joachim. issue resolved?
| Joachim. issue resolved?
| Pristionchus prl-1 mis-annotation
| https://github.com/WormBase/website/issues/1318
| Mary-Ann. issue resolved?
| wormbase-compara version is missing
| wormbase-compara version is missing

Revision as of 12:06, 19 September 2013


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.
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
extra zero in WB grant number https://github.com/WormBase/website/issues/1779 Verify?
old release gateway timeout https://github.com/WormBase/website/issues/1761 Todd, links to old releases return gateway timeout
How Do I ...?: see the tiling arrays? https://github.com/WormBase/website/issues/1685 looks resolved, close?
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.
BLAST not working for alignment to WS235 https://github.com/WormBase/website/issues/1443 Joachim. issue resolved?
wormbase-compara version is missing https://github.com/WormBase/website/issues/1231 Michael P. issue resolved?
BED file upload size limit? https://github.com/WormBase/website/issues/673 Todd. issue resolved?
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