Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
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= 2020 Meetings =
  
= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
== December 5, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
=== New interaction Venn diagram tool ===
 
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
 
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
 
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
 
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 
* Request: could there be a toggle to include/exclude high-throughput interactions?
 
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
 
  
 +
== June 4, 2020 ==
  
=== New round of phenotype requests ===
+
=== Citace (tentative) upload ===
* GMail really throttling email sending
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Chris will reach out to Google/GMail to see if we can:
+
* Citace upload to Hinxton on Friday, July 10th
** A) get a clear explanation about what their restrictions are and how they work and
 
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
 
  
=== Aligning interaction data with GO and GO-CAM ===
+
=== Caltech reopening ===
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
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* Paul looking to get plan approved
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
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* People that want to come to campus need to watch training video
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
+
* Masks available in Paul's lab
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
+
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
* Chris and Kimberly will meet to discuss further
+
** 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
  
=== Short SObA talk at Alliance meeting ===
+
=== Nameserver ===
* Raymond prepared to give short talk on SObA to the Alliance group
+
* 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
  
=== Single cell data visualization tool ===
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=== Alliance SimpleMine ===
* Eduardo will present to Paul's lab meeting tomorrow
+
* Any updates? 3.1 feature freeze is tomorrow
* Will discuss at Alliance expression working group pre-meeting
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* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call

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