Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== May 7, 2020 ==
 
  
=== Alliance COVID Page ===
+
== June 4, 2020 ==
* Available on stage
 
* Textpresso for Coronavirus up for testing
 
  
=== SimpleMine at Alliance ===
+
=== Citace (tentative) upload ===
* Still some confusion about what it is
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Will try to help clarify on PI meeting on Friday
+
* Citace upload to Hinxton on Friday, July 10th
  
=== Development environment for Alliance work ===
+
=== Caltech reopening ===
* Raymond and Juancarlos have been working on
+
* Paul looking to get plan approved
* Existing hardware is strained; set up virtual machine
+
* People that want to come to campus need to watch training video
* Still some technical issues
+
* 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
  
=== Open Publishing Festival ===
+
=== Nameserver ===
* Later this month
+
* Nameserver was down
* Micropublications involved
+
* CIT curators would still like to have a single form to interact with
* Organized by the Collaborative Knowledge Foundation
+
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
* Will involve publishers of books, journals, etc.
+
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
* Will have a MOD-focused event, would be good to have WB curators participate/attend
+
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
* Open to all
+
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
=== Genotype class ===
+
=== Alliance SimpleMine ===
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
+
* Any updates? 3.1 feature freeze is tomorrow
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 
* Would be good to be clear/transparent about which components were automatically inferred
 
 
 
=== WS277/278 ===
 
* Pipelines are pushed back by about 14 days/2 weeks
 

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