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]]
  
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
  
== May 7, 2020 ==
+
== June 4, 2020 ==
  
=== Alliance COVID Page ===
+
=== Citace (tentative) upload ===
* Available on stage
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Textpresso for Coronavirus up for testing
+
* Citace upload to Hinxton on Friday, July 10th
  
=== SimpleMine at Alliance ===
+
=== Caltech reopening ===
* Still some confusion about what it is
+
* Paul looking to get plan approved
* Will try to help clarify on PI meeting on Friday
+
* 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
  
=== Development environment for Alliance work ===
+
=== Nameserver ===
* Raymond and Juancarlos have been working on
+
* Nameserver was down
* Existing hardware is strained; set up virtual machine
+
* CIT curators would still like to have a single form to interact with
* Still some technical issues
+
* 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
  
=== Open Publishing Festival ===
+
=== Alliance SimpleMine ===
* Later this month
+
* Any updates? 3.1 feature freeze is tomorrow
* Micropublications involved
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* Organized by the Collaborative Knowledge Foundation
 
* Will involve publishers of books, journals, etc.
 
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 
* Open to all
 
 
 
=== Genotype class ===
 
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
 
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 
* 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
 
 
 
 
 
==May 13, 2020==
 
 
 
=== SURF students ===
 
* Welcome Fernando!
 
* Will work on neuron function with respect to dauer formation
 
 
 
=== Progress Report ===
 
* Review Google Doc from Paul to make sure you're latest updates are there
 
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
 
 
 
===Genotype class===
 
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
 
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
 
*Disease OA annotations now converted to the newly created genotypes where needed
 
*Need to work on disease dumper changes next
 
 
 
=== What genes should be linked to genotypes? ===
 
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
 
* What should we consider a "relevant gene"?
 
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
 
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
 
* For rearrangements, consider relevant any genes "inside" the rearrangement?
 
* For now, we will omit any genes from transgenes or rearrangements from being dumped into the "Gene" tag
 
* In the future, we may want to consider genes that have been specifically annotated as having some functional consequence and informs that the gene is of functional relevance to the genotype
 
 
 
=== Volunteer Community Curators ===
 
* Have had an additional 13 people volunteer
 
* Single one-on-one tutorial for someone in Hong Kong this past Monday
 
* Chris will hold a tutorial today and tomorrow for everyone else
 
* Have received many new community annotations from volunteers (and authors), validation still pending
 
 
 
=== Open Publishing Festival ===
 
* Ranjana will join as a panelist
 
* Other MOD curators will also join
 
* Festival calendar: https://openpublishingfest.org/calendar.html
 
 
 
=== Move to Chen building ===
 
* Scheduled for late January 2021
 
 
 
=== First completely virtual GO meeting ===
 
* Kimberly: went really well
 
* Only met 4 hours per day, due to time zone differences
 
* Had breakout sessions for focus groups
 
 
 
=== Alliance Literature Acquisition working group ===
 
* Plan to come up with use cases for OntoMate and Textpresso
 
**Ontomate link https://rgd.mcw.edu/QueryBuilder/
 
 
 
* Kimberly plans to draw up most common use cases for Textpresso
 
* Google doc for test cases: https://rgd.mcw.edu/QueryBuilder/getResult/?qFieldConditions%5B0%5D.fieldName=ontology&qFieldConditions%5B0%5D.fieldValue=Coronavirus%20infectious%20disease
 

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