Five year plan

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This page will serve as the starting place for developing a GMOD grant application, starting with items to work on in a five year plan.

Possible 5 year plan items

  • Expand cloud services from AWS to things like OpenStack and iPlant (and new, similar projects "iAnimal"?) like to end up here for example.
  • Develop generic ontology driven annotation tools that would allow annotation of any Chado data type (genotypes, phenotypes, natural diversity experiments, stocks, etc) (like (or exactly like) PomBase's Canto)
  • Develop or integrate existing tools (e.g. AmiGO2) for querying and visualising these ontology annotations
  • Develop tools for working with chromosomal rearrangements and related events (i.e. cancer), including visualization tools as well as standards for representing them in Chado.
  • Incorporate schema additions to extend Chado to clinical settings
  • Improve integration between core GMOD tools
  • Create component installers to allow users to use tools without having to download and configure prerequisites


  • JBrowse/WebApollo track sharing registry
  • Circular genome support
    • Cancer rearrangements
    • Circular dna (supported)
  • JBrowse synteny browser (mitch's prototype based on webGL)
  • JBrowse plugins
    • Primer designer, other analysis tools
    • restriction analysis
    • SAGE database
    • Direct UCSC connection
    • SeqWare workflow engine
  • DAS integration
  • "Transformation track"
  • create synthetic tracks of discontinuous regions


help desk aims:

  • keeping jBrowse healthy and GMOD healthy are closely related
  • help desk more focused on community outreach and training
    • jbrowse workshops?

iteroperability hackathons:

  • maker
  • galaxy

Three developement aims, one support aim:

  • one novel
  • two improvements
  • visualization
  • analysis

(missed part of this conversation)