Difference between revisions of "WBConfCall 2021.06.17-Agenda and Minutes"

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= Help Desk =
 
= Help Desk =
 
Open tickets:  
 
Open tickets:  
 +
 +
Phenotype:cortical granule exocytosis variant https://github.com/WormBase/website/issues/8279
 +
- Assigned to Gary Schindelman 
  
 +
I'd like to make a genome-wide graphic like the original 1998 C. elegans genome project paper https://github.com/WormBase/website/issues/8274 
 +
- Assigned to Scott Cain, looks like user is happy with Scott's sugestion of using jBrowse next gen 
 +
 +
Show DNA_text on WB Construct page https://github.com/WormBase/website/issues/8267
 +
- Assigned to Adam Wright
  
 
= Agenda and Minutes=
 
= Agenda and Minutes=
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= WS281 issues =
 
= WS281 issues =
 
* Empty assemblies[] in the ASSEMBLIES.WS281.json file
 
* Empty assemblies[] in the ASSEMBLIES.WS281.json file
 +
** Now raised as Ticket https://github.com/WormBase/website/issues/8280
 +
** HX will investigate and resolve this issue.
 
* discordant feature names in Ace and GFF for (at least some) Tier III species
 
* discordant feature names in Ace and GFF for (at least some) Tier III species
 +
** HX will unify the acedb and gff IDs so that the web code will not need to be changed.
  
  
 
=== Caltech ===
 
=== Caltech ===
 
==== CenGen  data ====
 
==== CenGen  data ====
 +
*GitHub #8075: https://github.com/WormBase/website/issues/8075
 
*Initially discussed to have the bar plot images going in as image data
 
*Initially discussed to have the bar plot images going in as image data
 
*CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
 
*CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
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*Can the files be stored on the ftp and the plots be displayed on the expression widget?
 
*Can the files be stored on the ftp and the plots be displayed on the expression widget?
 
*Bring in data both as pictures and interactive bar plots
 
*Bring in data both as pictures and interactive bar plots
 +
* Decided to put data on FTP. Daniela, Sibyl, Raymond will set up a meeting with Seth to get further insight of raw data and on how to reproduce the plots.
 +
* no need to remap, will be static connections to the genes provided by CenGen
 +
 +
==== Gene-Variation Associations ====
 +
*Caltech is not getting all of the gene-variation associations from the nightly geneace dump (e.g. some tm variation-gene associations are not in the OA curation tool)
 +
*If gene-variation associations are/will be made via the VEP pipeline that is part of the build, then we should get this information from each WS release?
 +
*We'd just like to confirm with Hinxton what the best strategy is
 +
*Associate WBGenes with 'tm' variations in nightly geneace variations file  https://github.com/WormBase/website/issues/8262
  
 
===Hinxton===
 
===Hinxton===
 +
 +
===IWM 2021===
 +
*WB workshop schedule - Date: Tuesday, June 22, 11:30 am - 1 pm (EDT); 8.30 am - 10 am (PDT); 4.30 pm - 6 pm (BST)
 +
<pre style="white-space: pre-wrap;
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white-space: -moz-pre-wrap;
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white-space: -pre-wrap;
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white-space: -o-pre-wrap;
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word-wrap: break-word">
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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
 +
 +
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
 +
 +
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
 +
 +
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
 +
 +
</pre>
 +
 +
*WB 2021 workshop folder: https://drive.google.com/drive/u/1/folders/1v0JsMvWW4NNkrSu60U--cgZW_Gj-5P2Y
 +
Presentations and other meeting info in this folder

Latest revision as of 16:28, 17 June 2021

Help Desk

Open tickets:

Phenotype:cortical granule exocytosis variant https://github.com/WormBase/website/issues/8279 - Assigned to Gary Schindelman

I'd like to make a genome-wide graphic like the original 1998 C. elegans genome project paper https://github.com/WormBase/website/issues/8274 - Assigned to Scott Cain, looks like user is happy with Scott's sugestion of using jBrowse next gen

Show DNA_text on WB Construct page https://github.com/WormBase/website/issues/8267 - Assigned to Adam Wright

Agenda and Minutes

WS281 issues

  • Empty assemblies[] in the ASSEMBLIES.WS281.json file
  • discordant feature names in Ace and GFF for (at least some) Tier III species
    • HX will unify the acedb and gff IDs so that the web code will not need to be changed.


Caltech

CenGen data

  • GitHub #8075: https://github.com/WormBase/website/issues/8075
  • Initially discussed to have the bar plot images going in as image data
  • CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
  • They can provide the underlying data and have the WB team generate interactive plots for each gene

We could: 1. bring the data files in OR 2. call the CenGen API on the fly

  • The first approach may be more work but better in the long run as we store the data
  • Can the files be stored on the ftp and the plots be displayed on the expression widget?
  • Bring in data both as pictures and interactive bar plots
  • Decided to put data on FTP. Daniela, Sibyl, Raymond will set up a meeting with Seth to get further insight of raw data and on how to reproduce the plots.
  • no need to remap, will be static connections to the genes provided by CenGen

Gene-Variation Associations

  • Caltech is not getting all of the gene-variation associations from the nightly geneace dump (e.g. some tm variation-gene associations are not in the OA curation tool)
  • If gene-variation associations are/will be made via the VEP pipeline that is part of the build, then we should get this information from each WS release?
  • We'd just like to confirm with Hinxton what the best strategy is
  • Associate WBGenes with 'tm' variations in nightly geneace variations file https://github.com/WormBase/website/issues/8262

Hinxton

IWM 2021

  • WB workshop schedule - Date: Tuesday, June 22, 11:30 am - 1 pm (EDT); 8.30 am - 10 am (PDT); 4.30 pm - 6 pm (BST)

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

12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources

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

12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A

Presentations and other meeting info in this folder