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
  
 +
= 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]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_December_2019|December]]
 
  
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== December 5, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== New interaction Venn diagram tool ===
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* [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?
 
  
=== New round of phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* GMail really throttling email sending
 
* Chris will reach out to Google/GMail to see if we can:
 
** 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 ===
 
* 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
 
* 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
 
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 
* Chris and Kimberly will meet to discuss further
 
  
=== Short SObA talk at Alliance meeting ===
+
== June 4, 2020 ==
* Raymond prepared to give short talk on SObA to the Alliance group
 
  
=== Single cell data visualization tool ===
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=== Citace (tentative) upload ===
* Eduardo will present to Paul's lab meeting tomorrow
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Will discuss at Alliance expression working group pre-meeting
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* 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
  
== December 19, 2019 ==
+
=== 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
  
=== AGR Face to Face meeting debrief ===
+
=== Alliance SimpleMine ===
* AGR data need to synchronize with MODs. AGR will have more frequent releases (monthly or every two months) so that it reflects the same data as MODs.
+
* Any updates? 3.1 feature freeze is tomorrow
* MODs have different curation policies. For example, BioGrid has predicted protein-protein interactions. AGR import them but WormBase does not have them. AGR needs to do its own prediction based on the current data, although BioGrid does a good job.
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* The gene description curation tool developed by Juancarlos got good feedback. Juancarlos will add more function to visualize and compare annotations.
 
* The gene description working group will enter maintenance mode.
 
* Allele phenotype WG will start to the AGR allele page.
 
* SimpleMine vs intermine: Wen argues that there is no conflict. It is like 7-Eleven vs. Walmart (and Biomart is like Target ...)
 
* High-throughput expression: Most of MODs have zero curation manpower thus they prefer to outsource to Express Atlas or GEO unless future grants prioritize curation on high-throughput. Expression Atlas regard worm as a low priority so they may not do much for the worm.
 
* Software development: focus on AGR instead of MODs. SAB hopes all MODs to retire their features to turn more users to AGR.  
 
* WormBase should direct all links of orthologs to AGR. Currently, orthologs are pointed to a WormBase page with no content. Wen will create a github ticket for the web team to make the changes.
 
* Paper triage working group: It will be good if MODs can share their paper sources. Karen, Michael Mueller, and Kimberly will be involved in this WG.
 
* Working Groups need more cross-talks, for example, GO and gene description are related.
 
* SoBA got positive feedback. Some groups want to use it to compare two-gene curations, as well as the enrichment analysis.
 
* Non-coding RNA: Paul Sternberg will contact Frank Slack to see what they need for curation.
 

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