WebDev 2016.02.23-Agenda and Minutes

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Administrative notes

Web development

-WS252 widget related issues mostly resolved, except (please don't cache them):

  • genetic widget on variation page and
  • Sequence widgets on CDS, transcript, protein (working on a bug fix)

- Issues with multiple strains (bioproject) from the same species are resolved.

  • they have own species index page, ftp links, gbrowse links
  • integrated search for their gene and protein under their strain (not mixed up with the default strain)

- Had conversation with GO people about gene model graph, will work on this visualization after WS252 development

- Will discuss with Daniala and TransgeneOme about pulling data from their API

Data visualization

  • committed gbrowse config files for WS252

- jbrowse:

  • jq tool:
    • really easy to insert a field into all JSON objects
    • doubles as a JSON validator, helped fixing some formatting issues
  • found and fixed 2 missing tracks for WS252
  • Installed test instance of JBrowse 1.12.0 (currently using 1.11.6)
  • Working with WebApollo people on handling subtracks, there is an example in the 1.12.0 test instance here. Note that several issues remain, the most notable of which is that it won't draw data until you zoom or pan around.

Database migration

- Working with Juancarlos to get him access to Datomic REST API - Split repo into one repo per project:

  • ACeDB to Datomic
  • ...

- Will finish setting up DynamoDB ready to run ACeDB to Datomic, needs to:

  • configure transactor for DynamoDB
  • setup permission
  • wait on model file from hinxton

- Working on documentation

Intermine / InterMOD progress

Outstanding issues

Nothing needs discussion.