Difference between revisions of "WBConfCall 2016.03.17-Agenda and Minutes"

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* Datomic (Adam)
 
* Datomic (Adam)
 
* Visualizing human variations on worm genome (Siby)  
 
* Visualizing human variations on worm genome (Siby)  
* JBrowse (Scott)
+
* JBrowse & GBrowse (Scott) Looking at up grading to recent release of JBrowse, includes [http://dev.wormbase.org:10004/?data=data%2Fc_elegans_simple&loc=I%3A9859465..9880430&tracks=PHA-4%20(Pol%20II%20ChIP)%3A%20Combined%2CCurated%20Genes%20(protein%20coding)%2CCurated_Genes&highlight= "fancier" glyphs and subtracks that don't quite work] :-/ (the subtracks only load after you pan from the original starting position)
 +
** Scott will write a tutorial for uploading and sharing data
 +
** Will also inquire about JBrowse supporting UCSC track hub
  
 
== OMIM linking to WormBase ==
 
== OMIM linking to WormBase ==
Line 15: Line 17:
  
 
=Minutes=
 
=Minutes=
 +
== Progress update by web team members ==
 +
* (Todd can't make today's call due to a conflict with RRID call)
 +
=== Datomic (Adam) ===
 +
* Transitioning Datomic build process to EBI team
 +
* Setting up website to partially backed by Datomic
 +
* Will have a version of the website running partially on Datomic available for testing
 +
* Q: what does DynamoDB do?
 +
**  A: it runs the production Datomic database on Amazon cloud. It’s intended for high performance and low maintenance.
 +
 +
=== Visualizing human variations on worm genome (Siby)===
 +
* creating a schematic drawing for human and worm gene comparison and map variations onto it
 +
* getting alignment and annotation (exon and domain) from ParaSite API
 +
* will have a prototype ready for testing in a week
 +
* will check out Ensembl REST API for mapping and searching by variation RRSID
 +
 +
=== JBrowse & GBrowse (Scott)===
 +
* Looking at up grading to recent release of JBrowse, includes [http://dev.wormbase.org:10004/?data=data%2Fc_elegans_simple&loc=I%3A9859465..9880430&tracks=PHA-4%20(Pol%20II%20ChIP)%3A%20Combined%2CCurated%20Genes%20(protein%20coding)%2CCurated_Genes&highlight= "fancier" glyphs and subtracks that don't quite work] :-/ (the subtracks only load after you pan from the original starting position)
 +
** Scott will write a tutorial for uploading and sharing data
 +
** Will also inquire about JBrowse supporting UCSC track hub
 +
 +
=== OMIM linking to WormBase ===
 +
From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know?
 +
* EBI will run code that replaces the outdated file with symlinks to files built in the latest release
 +
* Ranjana and Paul will communicate with OMIM about the options for updating the links
 +
 +
==Unresolved Help Desk Issues==
 +
* Many thanks to you all for helping me answering questions submitted to help desk!
 +
* gene_interactions FTP file not made during website staging process [https://github.com/WormBase/website/issues/4655 4655]
 +
** Todd and Sibyl will work on
 +
* Account email & password reset request  [https://github.com/WormBase/website/issues/4659 4659]
 +
** Todd and Sibyl will come up with protocol for: password and user email reset for WormBase account and migrating existing account to 3rd party login
 +
* transpozable element sequence
 +
** Q: How to get the full sequence (not just the mRNA region)
 +
***A: not available as a precomputed file. User has to parse the GFF and sequence file to get it.

Latest revision as of 17:29, 17 March 2016

Agenda

Progress update by web team members

  • (Todd can't make today's call due to a conflict with RRID call)
  • Datomic (Adam)
  • Visualizing human variations on worm genome (Siby)
  • JBrowse & GBrowse (Scott) Looking at up grading to recent release of JBrowse, includes "fancier" glyphs and subtracks that don't quite work :-/ (the subtracks only load after you pan from the original starting position)
    • Scott will write a tutorial for uploading and sharing data
    • Will also inquire about JBrowse supporting UCSC track hub

OMIM linking to WormBase

From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know?

Unresolved Help Desk Issues

  • Many thanks to you all for helping me answering questions submitted to help desk!
  • gene_interactions FTP file not made during website staging process 4655
  • Account email & password reset request 4659

Minutes

Progress update by web team members

  • (Todd can't make today's call due to a conflict with RRID call)

Datomic (Adam)

  • Transitioning Datomic build process to EBI team
  • Setting up website to partially backed by Datomic
  • Will have a version of the website running partially on Datomic available for testing
  • Q: what does DynamoDB do?
    • A: it runs the production Datomic database on Amazon cloud. It’s intended for high performance and low maintenance.

Visualizing human variations on worm genome (Siby)

  • creating a schematic drawing for human and worm gene comparison and map variations onto it
  • getting alignment and annotation (exon and domain) from ParaSite API
  • will have a prototype ready for testing in a week
  • will check out Ensembl REST API for mapping and searching by variation RRSID

JBrowse & GBrowse (Scott)

  • Looking at up grading to recent release of JBrowse, includes "fancier" glyphs and subtracks that don't quite work :-/ (the subtracks only load after you pan from the original starting position)
    • Scott will write a tutorial for uploading and sharing data
    • Will also inquire about JBrowse supporting UCSC track hub

OMIM linking to WormBase

From Ranjana: Kevin and Paul D, I see that you both are working on this (#4656 on GitHub), for WS253? Would you please get in touch with OMIM to let them know?

  • EBI will run code that replaces the outdated file with symlinks to files built in the latest release
  • Ranjana and Paul will communicate with OMIM about the options for updating the links

Unresolved Help Desk Issues

  • Many thanks to you all for helping me answering questions submitted to help desk!
  • gene_interactions FTP file not made during website staging process 4655
    • Todd and Sibyl will work on
  • Account email & password reset request 4659
    • Todd and Sibyl will come up with protocol for: password and user email reset for WormBase account and migrating existing account to 3rd party login
  • transpozable element sequence
    • Q: How to get the full sequence (not just the mRNA region)
      • A: not available as a precomputed file. User has to parse the GFF and sequence file to get it.