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
iteroperability hackathons:
Three developement aims, one support aim:
- one novel
- two improvements
- visualization
- analysis
(missed part of this conversation)
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