WBConfCall 2016.03.17-Agenda and Minutes

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• EBI will run code that replaces the outdated file with symlinks to files built in the latest release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.