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.|
|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|