Core Cytoscape Feature Prioritization

Date: Saturday, July 19, 2008


Detailed list of tasks to push ahead with OSGi adoption and assessment. Names and estimated deadlines included.


  1. build system - easy to use for plugin developers (Kei - end of Aug)
    • setup repository
    • documentation on wiki for a naive developer
    • maven site documentation
    • debugging in eclipse (other IDEs) must be easy for plugin developers (ISB - end of Aug)
    • testing of core and plugin development process by core and naive developers (AlexP, Allan, Scooter, Mr.X - mid Sept)
    • test web start (see

    • develop templates/demos for plugin interoperability, dependency, extension, multiple versions coexisting, etc.
  2. Cytoscape Presence (ISB + AlexP, Kristina - December?)
    • collect materials: video ideas, tutorials, course material, selected publications (scivee?)
    • build, identify infrastructure for this material
    • deploy
    • discuss consistency/style guidelines
  3. Cleaning up all warnings and mvn find bugs (Everyone!)
    • a lot of these are unchecked errors
    • site hackathon?
    • split up arbitrarily
  4. GraphPerspective <-- new CyNetwork (Mike -> Everyone!)

    • implications for CyNodeAttributes, CyEdgeAttributes

    • work out details for selection, hide=>remove; this has implications in other places that relied on "hide"

    • this directly addresses the new "copy model" versus root graph model
    • this is not a simple find/replace

    • Mike can do some initial work on it and then slice and dice and toss it to the team
  5. ViewModel

    • design should follow GraphPerspective work (~ 6 months out)

    • has implications for Presentation layer and dependencies that require decisions about the Presentation Layer
  6. I/O Layer (Input from AlexA, Scooter, Brian, Thomas?)
    • TBD
    • requires feedback on current discussion and API proposals (see Saturday retreat agenda links)
  7. Command
    • TBD
    • Kei and Scooter may have prior art that can implemented now
  8. Concurrency
    • TBD
    • perhaps we should wait to see where the critical asynchronous use cases are before defining where to focus
    • we could restrict asynchronous events only to thread safe (should we add thread safety at all?)
    • goal: thread safe core
    • documentation will be important for developers to know how to thread and what to look out for


CytoscapeRetreat2008/FeaturePrioritization (last edited 2009-02-12 01:03:51 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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