Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Discussion topics: | * Discussion topics: | ||
** Creating more transparency/communication in the Alliance DQM data submission process for QC | ** Creating more transparency/communication in the Alliance DQM data submission process for QC | ||
+ | *** Can there be a landing page for all uploaded files to check? | ||
*** JSON or TSV, etc.? | *** JSON or TSV, etc.? | ||
− | |||
=== Genotype === | === Genotype === |
Revision as of 19:43, 27 February 2020
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2020 Meetings
February 6, 2020
Worcester Area Worm Meeting talk
- Confirmed for December 2020 or February 2021
Alaska software
- Code developed and maintained by Joseph, but not long term solution
- Raymond and Eduardo talked about taking it over
- Why have a web application vs. a command-line application?
- Wanted to make it easy, but also to capture meta data for WB
- Should/will find out from Joseph about how hard it is to maintain the software
- Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
- Expression working group working with Brian Oliver to have GEO take in more structured meta data
- Array Express tried requiring more structured meta data, but authors stopped submitting
- May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
February 13, 2020
Alliance Literature Group
- Held first meeting on Monday, February 10th
- Regular meetings will be on Tuesdays at 10am/1pm/6pm
- Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
- Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
?Genotype class model
- Proposal
- Can aim to implement for WS277 but may have to wait until WS278
Genotype OA
- Will put documentation here
WB All-Hands Meeting
- Doodle poll
- Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
February 20, 2020
Genotype
- We will equate superficially similar/identical genotypes for now
- What if labs sequence strains later and find out more?
- Labs will have to report strains and their sequence and we back-curate accordingly
VC2010 assembly genes
- WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
- How to best handle these "extra" genes?
- We could make different species entries that specify the assembly version
February 27, 2020
WB Project meeting
- Early May (~May 7th, 8th)
- Discussion topics:
- Creating more transparency/communication in the Alliance DQM data submission process for QC
- Can there be a landing page for all uploaded files to check?
- JSON or TSV, etc.?
- Creating more transparency/communication in the Alliance DQM data submission process for QC
Genotype
- Genotype Wiki page updated
- Will start building Genotype OA
Outreach inbox
- 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
- Many are bounced emails messages
- Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
New nameserver issues
- Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
- Should be getting dumped nightly to Postgres, but something seems to be wrong
- Ranjana added a list of strains last week, but still doesn't see them in the OA
- Daniela has been using the old CGI to add in new variation objects to Postgres
- These objects are coming up when querying the nameserver, but not showing up in OA
GO CAM/Noctua modeling
- Should be major improvements in Noctua in place after recent hackathon
- Would be good to make a big push on curating models; e.g. signalling pathways that act somewhat differently in different cell types (in same organism) and in different organisms (e.g. Wnt signaling)