Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Progress Report === | === Progress Report === | ||
* Review Google Doc from Paul to make sure you're latest updates are there | * Review Google Doc from Paul to make sure you're latest updates are there | ||
− | * Doc here: | + | * Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing |
===Genotype class=== | ===Genotype class=== |
Revision as of 18:05, 14 May 2020
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2020 Meetings
May 7, 2020
Alliance COVID Page
- Available on stage
- Textpresso for Coronavirus up for testing
SimpleMine at Alliance
- Still some confusion about what it is
- Will try to help clarify on PI meeting on Friday
Development environment for Alliance work
- Raymond and Juancarlos have been working on
- Existing hardware is strained; set up virtual machine
- Still some technical issues
Open Publishing Festival
- Later this month
- Micropublications involved
- 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?
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