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| [[WormBase-Caltech_Weekly_Calls_January_2020|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] |
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− | | + | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] |
− | == February 6, 2020 ==
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− | === Worcester Area Worm Meeting talk ===
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− | * Confirmed for December 2020 or February 2021
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− | === Alaska software ===
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− | * Code developed and maintained by Joseph, but not long term solution
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− | * Raymond and Eduardo talked about taking it over
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− | * Why have a web application vs. a command-line application?
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− | ** Wanted to make it easy, but also to capture meta data for WB
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− | * Should/will find out from Joseph about how hard it is to maintain the software
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− | * Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
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− | * Expression working group working with Brian Oliver to have GEO take in more structured meta data
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− | * Array Express tried requiring more structured meta data, but authors stopped submitting
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− | * May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
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− | == February 13, 2020 ==
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− | | |
− | === Alliance Literature Group ===
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− | * Held first meeting on Monday, February 10th
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− | * Regular meetings will be on Tuesdays at 10am/1pm/6pm
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− | * Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
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− | * Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
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− | | |
− | === ?Genotype class model ===
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− | * [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
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− | * Can aim to implement for WS277 but may have to wait until WS278
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− | | |
− | === Genotype OA ===
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− | * Will put documentation [[Genotype|here]]
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− | | |
− | === WB All-Hands Meeting ===
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− | * [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
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− | * Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
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− | | |
− | | |
− | == February 20, 2020 ==
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− | | |
− | === Genotype ===
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− | * We will equate superficially similar/identical genotypes for now
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− | * What if labs sequence strains later and find out more?
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− | * Labs will have to report strains and their sequence and we back-curate accordingly
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− | | |
− | === VC2010 assembly genes ===
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− | * WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
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− | * How to best handle these "extra" genes?
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− | * We could make different species entries that specify the assembly version
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− | | |
− | | |
− | == February 27, 2020 ==
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− | | |
− | === WB Project meeting ===
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− | * Early May (~May 7th, 8th)
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− | * Discussion topics:
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− | ** Creating more transparency/communication in the Alliance DQM data submission process for QC
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− | *** Can there be a landing page for all uploaded files to check?
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− | *** JSON or TSV, etc.?
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− | | |
− | === Genotype ===
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− | * [[Genotype|Genotype Wiki page]] updated
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− | * Will start building Genotype OA
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− | | |
− | === Outreach inbox ===
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− | * 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
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− | * Many are bounced emails messages
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− | * 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.
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− | | |
− | === New nameserver issues ===
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− | * Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
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− | * Should be getting dumped nightly to Postgres, but something seems to be wrong
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− | * Ranjana added a list of strains last week, but still doesn't see them in the OA
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− | * Daniela has been using the old CGI to add in new variation objects to Postgres
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− | * These objects are coming up when querying the nameserver, but not showing up in OA
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− | | |
− | === GO CAM/Noctua modeling ===
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− | * Should be major improvements in Noctua in place after recent hackathon
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− | * 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)
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− | | |
− | === SObA ===
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− | * Raymond working on writing paper
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− | * While reviewing pipeline, Raymond encountered some issues
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− | * Seth suggested using Docker
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− | * Raymond wants to go through and explain the development pipeline from the beginning
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− | | |
− | === Alaska ===
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− | * Stalled; no word from Joseph
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