Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== February 6, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== Worcester Area Worm Meeting talk ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* 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 ==
+
== June 4, 2020 ==
  
=== Alliance Literature Group ===
+
=== Citace (tentative) upload ===
* Held first meeting on Monday, February 10th
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
+
* Citace upload to Hinxton on Friday, July 10th
* 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 ===
+
=== Caltech reopening ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
+
* Paul looking to get plan approved
* Can aim to implement for WS277 but may have to wait until WS278
+
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
=== Genotype OA ===
+
=== Nameserver ===
* Will put documentation [[Genotype|here]]
+
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
=== WB All-Hands Meeting ===
+
=== Alliance SimpleMine ===
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
+
* Any updates? 3.1 feature freeze is tomorrow
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
 
 
 
== 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
 

Revision as of 00:09, 5 June 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call