Difference between revisions of "WBConfCall 2013.09.19-Agenda and Minutes"
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2. ORCID for WBPerson ? | 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 | ||
+ | * 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 | ||
= Help Desk issues = | = Help Desk issues = |
Revision as of 08:40, 19 September 2013
Agenda
1. WormBase development environment for Caltech. (local installation / access to OICR dev / Amazon AMI)
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
- 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
Help Desk issues
Dealing with Natural Variation - from Marie-Anne Felix. (Mary Ann/Kev) | https://github.com/WormBase/website/issues/1735 | Would be good if interested parties could think about the issues before the meeting. I've added a few of my own comments. |
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? |
Pristionchus prl-1 mis-annotation | https://github.com/WormBase/website/issues/1318 | Mary-Ann. 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 |