WBConfCall 2017-10-05-Agenda and Minutes

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outstanding help desk items

These are all new--thanks everybody for staying on top of these.

  • None!

Adding links to AGR gene and disease pages


  • Should have similar link structure at each mod?
  • mock ups of a few options would be good (link here)
  • if the goal is to raise awareness (it is), link text should contain "Alliance of Genome Resources" and even a logo

Splicing frequency diagrams

  • Denis Dupuy presented work at the IWM about depicting gene splicing frequencies derived from RNA-Seq data on a log-scale
  • These depictions are often useful for deciding which splice variant(s) is/are the most prevalent, especially for genes with many splice variants
  • His paper has been submitted and is expected to be accepted soon
  • He has sent us images (in PDF) for each gene in C. elegans
  • Gary W. has started working out a similar display for all species
  • Do we want to display these images on gene pages?
  • Some examples:
    • daf-16 on WB GBrowse:

Daf-16 locus GBrowse.png

    • daf-16 splicing frequencies from Denis:

Daf-16 DD splcing frequencies.png

    • hlh-30 on WB GBrowse:

Hlh-30 locus GBrowse.png

    • hlh-30 splicing frequencies from Denis:

Hlh-30 DD splcing frequencies.png

JBrowse posibilities

It is certainly possible to do graph type things in JBrowse. See this example GWAS viewer plugin: Gwasplotter.png


  • The display from the authors is (IMHO Scain (talk) 16:04, 5 October 2017 (UTC)) difficult to interpret; if we want to provide similar data in the genome browser or gene page we should probably create a cleaner representation
  • Discussion will continue with authors, Gary, Chris and Scott


About AGR


  • "Site visit" next spring, evaluate progress and decide how to proceed with funding.
  • We need to push and be effective.

NAR Paper

Back from review; stuff to do

Thoughts about leaving FMap

  • in many respects, JBrowse would suffice, or Apollo