WebDev 2016.03.22-Agenda and Minutes

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JBrowse & GBrowse

  • Working on tutorial for uploading and sharing data in JBrowse
  • Trying to figure out how to deal with making a persistant popup balloon in GBrowse in light of the default link configuration (they are incompatible)
    • Adam suggested writing a JS hack to intercept the link and display the balloon--that might work.


  • Have development website running off off Clojure API for the Gene page and pulling data from Datomic+DynamoDB
  • Rest work--found a Clojure module that may help making a more standard rest interface (datomic-to-catalyst REST API)
  • things to think about:
    • where to place tests for API code that has been ported to Clojure. There are tests that are failing now on the Datomic branch of the website because it is no longer pulling specific information from AceDB. We will need to remove no-longer-required tests and make new ones to test the Datomic data withing the Catalyst tests. Also we will need to start thinking about writing tests for the Clojure API Code.


  • Continue working on Visualizing Human Variations feature:
    • Getting data from Parasite: homology, aligned sequence, exon and domain position
      • Created a small client to fetch and temporarily storing data for use in a variety of places
    • (WIP) convert coordinates and draw graphic based on the actual data
    • Problems to resolve:
      • how to handle multiple splice variants
      • how to handle overlapping domain assignments by multiple standards
      • ensure DNA alignment and protein alignment can align correctly to each other