Difference between revisions of "WormBase-Caltech Weekly Calls"

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== 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 ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
* Can aim to implement for WS277 but may have to wait until WS278
=== Genotype OA ===
* Will put documentation [[Genotype|here]]
=== WB All-Hands Meeting ===
* [https://doodle.com/poll/7f65p4ba6d88ztzt 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.?
=== Genotype ===
* [[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)
=== SObA ===
* Raymond working on writing paper
* While reviewing pipeline, Raymond encountered some issues
* Seth suggested using Docker
* Raymond wants to go through and explain the development pipeline from the beginning
=== Alaska ===
* Stalled; no word from Joseph

Revision as of 15:21, 3 March 2020