Difference between revisions of "WBConfCall 2023.05.04-Agenda and Minutes"

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= Agenda and Minutes =
 
= Agenda and Minutes =
 +
 +
== HelpDesk ==
 +
* https://github.com/WormBase/website/issues/9034
  
 
== scRNA from Whole-body gene expression atlas of an adult metazoan ==
 
== scRNA from Whole-body gene expression atlas of an adult metazoan ==
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** Link out to their web site and analysis tools (planned)
 
** Link out to their web site and analysis tools (planned)
 
** Inclusion on http://single-cell.wormbase.org/
 
** Inclusion on http://single-cell.wormbase.org/
 +
*** if we have the files in .h5ad format we can try to set it up
 
** Likely house keeping genes
 
** Likely house keeping genes
 +
*** these could be brought in via expression cluster
 
** Makers used for cell cluster ID
 
** Makers used for cell cluster ID
 +
*** integrate into anatomy pages
 
** Ligand-receptor expression informed cell-cell interaction
 
** Ligand-receptor expression informed cell-cell interaction
 +
*** for this and the following items Hinton does not have enough manpower to deal with it
 
** Transcription factor code per cell type
 
** Transcription factor code per cell type
 +
** cis-acting sites for cell types
 +
 +
== IWM ==
 +
* Booth
 +
** received this morning an email from the contractor for booth logistics
 +
*** carpeting
 +
*** electrical and extension cords
 +
**** Stavros Sarah can bring some extension cords
 +
*** furniture
 +
**** Sarah and Stavros can bring camping chairs
 +
* Swag
 +
** General WB swag
 +
** Community curation swag
 +
** microPublication swag
 +
** https://docs.google.com/document/d/1v8bCoL2Qy9hNQmJ57YOccg8HkmKXclulugfnYwGU7lM/edit
 +
* Workshop
 +
** Scott will be remote
 +
** Check in with Todd if he can give the tools talk
 +
 +
== Orthology ==
 +
* Alliance and WB results differ, that influences the gene descriptions
 +
* Need a manual assertion of homology using manually written concise descriptions?
 +
 +
== Name Server ==
 +
* Any update on this, Todd?
 +
 +
== Caltech server with WormBase name ==
 +
Valerio will test, then write to Todd

Latest revision as of 17:22, 4 May 2023

Agenda and Minutes

HelpDesk

scRNA from Whole-body gene expression atlas of an adult metazoan

  • Web site https://wormseq.org/
  • Curatable data (need to decide what to take on)
    • Interactive graph TPM / % cell expressing per gene (planned)
    • Enriched gene set per cell (planned)
    • Link out to their web site and analysis tools (planned)
    • Inclusion on http://single-cell.wormbase.org/
      • if we have the files in .h5ad format we can try to set it up
    • Likely house keeping genes
      • these could be brought in via expression cluster
    • Makers used for cell cluster ID
      • integrate into anatomy pages
    • Ligand-receptor expression informed cell-cell interaction
      • for this and the following items Hinton does not have enough manpower to deal with it
    • Transcription factor code per cell type
    • cis-acting sites for cell types

IWM

  • Booth
    • received this morning an email from the contractor for booth logistics
      • carpeting
      • electrical and extension cords
        • Stavros Sarah can bring some extension cords
      • furniture
        • Sarah and Stavros can bring camping chairs
  • Swag
  • Workshop
    • Scott will be remote
    • Check in with Todd if he can give the tools talk

Orthology

  • Alliance and WB results differ, that influences the gene descriptions
  • Need a manual assertion of homology using manually written concise descriptions?

Name Server

  • Any update on this, Todd?

Caltech server with WormBase name

Valerio will test, then write to Todd

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