Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
== May 13, 2021 ==
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
=== Textpresso supplement ===
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* Due Monday
 
* Michael working with Paul S
 
  
=== AWS credits ===
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* Michael and Valerio were awarded AWS credits, more than they can use
 
* Maybe they can be repurposed
 
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
 
  
=== Automated gene descriptions ===
 
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
 
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
 
* May be the focus of an Alliance supplement
 
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
 
  
=== IWM 2021 WB Workshop ===
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== September 2, 2021 ==
* Scheduled for June 22, 2021
 
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
 
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
 
* Here is the submitted workshop schedule:
 
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
 
  
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
 +
Needed for
 +
*AFP community curation
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*microPublication author tracking for all species
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
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Problems:  
 +
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
 +
*need to do this outside of Alliance  
  
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
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Action
 +
*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
  12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
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Will do
 +
*create biolink model based on current WB postgres/Caltech model
 +
*Adam will add tables when we have them
 +
 
 +
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
 +
 
 +
== September 16, 2021 ==
 +
 
 +
1. CeNGEN enriched genes per cell type data targeted for WS283.
 +
 
 +
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.
 +
 
 +
== September 23, 2021 ==
 +
 
 +
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
 +
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
 +
* Update the WB page on citing WormBase
 +
 
 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 2021

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September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.