RFC Name : Cytoscape Commons

Editor(s): DanielAbel (feel free to sign up :) )

Date: …

Status: draft


Provide some infrastructure for plugin developers: automated builds for plugins, maybe even wiki/bugtracker/version control hosting.


Some cytoscape plugins are neglected and even for the most popular ones it is tedious to find their version control system / sourcecode, and in many cases they don't have a wiki or a bugtracker.

Use Cases

Implementation Plan

Outline and describe the process and major issues related to implementing this proposal. Illustrate your plan when possible. Try this free online tool for making diagrams -> Best4c (draw; save; then insert hyperlink into this page)

There is basically two options:

  1. provide our own hosting. This means creating a google code / sourceforge-like site. This might be a lot of work, or it might be as

    simple as setting up drproject or trac or something similar.

  2. Don't provide hosting for wiki/version control/bugtracker, just provide automated builds. Point plugin developers to google code, and write easy-to-follow tutorials to set up a google code project and tie it in with cytoscape's automated build.

With 2), we only need to extend the plugin metadata format (plugin.props) to include the necessary metadata

Advantages of 1): possibly easier to tie in plugin's bugtracker into AutomaticBugReporter, or to move tickets from cytoscape's system to the plugin's system (i.e. reclassify a bug submitted to cytoscape.org as a bug in some plugin).

Project Management

Project Timeline

Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> Help-u-Plan (create a new chart; modify; right-click to save gif; then attach to this page)

Tasks and Milestones

Outline the major milestones and tasks involved in implementation.

  1. Milestone 1: find out possible disadvantages of 'don't have own hosting' option

    1. Task 1: check whether tickets can be moved from cytoscape's system to a google code project's tracker
    2. Task 2: check whether AutomaticBugReporter will be able to submit tickets to a google code project's tracker

  2. Milestone 3: rethink plugin.props: what parts of it will be handled by OSGi / P2

    1. versioning will apparently done by OSGi instead of the plugin.props
  3. Milestone 2: set up automated builds for plugins

    1. configure automatic build system
    2. create/configure summary page that shows results
  4. Milestone 2: write / extend plugin developer's documentation

    1. document how to optimally configure this with Eclipse / other IDEs (include things like setting up mylyn to manage tickets from IDE, if possible)
  5. move code from csplugins directory of svn to this new system

Project Dependencies

Similar sites

Other open-source projects have similar sites for library/module/plugin authors. We should look to these for ideas and possible alternatives:

Comparison of hosting alternatives

i.e. hosting the wiki,version control and tickets. Not automatic builds.

See comparison of free hosting places on wikipedia The following is a quick summary based on our needs:



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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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