Five year plan

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

• 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

notes

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)