Difference between revisions of "WBConfCall 2017-10-05-Agenda and Minutes"

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These are all new--thanks everybody for staying on top of these.
 
These are all new--thanks everybody for staying on top of these.
  
−
* Does C. elegans have a functioning nervous system? https://github.com/WormBase/website/issues/5885
+
* None!
−
* Spell download tables? https://github.com/WormBase/website/issues/5887
+
 
 +
== Adding links to AGR gene and disease pages ==
 +
* It has been requested that, for the October 20th AGR 1.0 release, we have prominent links to AGR gene pages from MOD gene pages and prominent links to AGR disease pages from MOD disease pages
 +
* To be determined:
 +
** Where exactly should the link go? In the Overview widget? External Links widget (although may not be prominent enough)?
 +
** Should the link be represented by the AGR logo? The entire phrase "Alliance of Genome Resources"? Just "Alliance" or "AGR"?
 +
** We can have a tooltip/pop-up when hovering the cursor over the link to spell out "Alliance of Genome Resources"
 +
* Some slides with mockups/summary: https://docs.google.com/presentation/d/1yfEvYXEMyfKy260YYMQprqoIfMpfMAVUhmzu-1vuPdU/edit?usp=sharing
 +
* Have created GitHub tickets:
 +
** https://github.com/WormBase/website/issues/5875
 +
** https://github.com/WormBase/website/issues/5876
 +
 
 +
===Notes===
 +
*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:
 +
[[File:Daf-16_locus_GBrowse.png]]
 +
** daf-16 splicing frequencies from Denis:
 +
[[File:Daf-16_DD_splcing_frequencies.png|900px]]
 +
** hlh-30 on WB GBrowse:
 +
[[File:Hlh-30_locus_GBrowse.png]]
 +
** hlh-30 splicing frequencies from Denis:
 +
[[File:Hlh-30_DD_splcing_frequencies.png|1230px]]
 +
 
 +
===JBrowse posibilities===
 +
It is certainly possible to do graph type things in JBrowse.  See this example GWAS viewer plugin:
 +
[[File:gwasplotter.png|1000px]]
 +
 
 +
===Notes===
 +
*The display from the authors is (IMHO [[User:Scain|Scain]] ([[User talk: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
  
 
=Minutes=
 
=Minutes=
 +
 +
==About AGR==
 +
 +
===notes===
 +
*"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

Latest revision as of 16:04, 5 October 2017

Agenda

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

Notes

  • 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

Notes

  • 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

Minutes

About AGR

notes

  • "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
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