|
|
| Line 28: |
Line 28: |
| | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] |
| | | | |
| − | | + | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] |
| − | == 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
| |
