Developer Documents

Get Involved!

Cytoscape App Developer Ladder

Start your climb today! This is the best introduction to Cytoscape App development.

Publish Your Apps

Got a new App? Please send it to us. Once your plugin is registered to the store, Cytoscape users can access it through App Manager.

Google Summer of Code

If you are a student, you can contribute to Cytoscape through Google Summer of Code program. For more information about GSoC, please visit NRNB web site.

Join Core Team

Want to hack the Cytoscape Core code? Volunteers are always welcome! Joining our community is easy. There's no commitment beyond writing good code and you can contribute as much or as little as you like. Here is how to get started:

  • Check out our Product Roadmap to see where we've been and where we're heading.
  • Ask questions and start sending us pull-requests / patches on the cytoscape-helpdesk mailing list.
  • We'll provide commit access to our GitHub repository once we trust you!
  • Start joining our team conference calls each Thursday to coordinate your development efforts with ours. Contact us for details on calling in.
  • If you remain a helpful contributor to the team, we'll vote you in as a core developer!
  • If your company or institution is interested in taking a larger role in the project, join the Cytoscape Consortium. Please contact us for more details.

Developer Resources

Issue Tracker, Nexus Repository, Nightly Builds, and Code Metrics is the start page for all developers. You can cehck the most up-to-date information about Cytoscape Core projects from here.

Code Repository on GitHub

Cytoscape Core projects are now hosted on GitHub. From now on, latest version of Cytoscape code should be obtained from the following git repositories:

(Desupported) Cytoscape 2.x

Note that Cytoscape 3 is a multi-repository project. You need to read this document to learn how to clone all Cytoscape 3 projects.

Port Your 2.x Plugins

With the release of the 3.x, Cytoscape core team no longer maintaining 2.x code and you need to port your Plugins to 3.x series to use latest features in Cytoscape. In the sections below, you'll find links to documentation and tutorials related to 3.x app development.


Cytoscape Helpdesk Google Group is the best way to reach core developers. If you have any App development questions, please send it to the mailing list.

Documentation for 3.x App Developers

What is Cytoscape 3.x?

Learn about the Architecture, Backward Compatibility, and API of Cytoscape 3.x.

What is the Cytoscape 3.x Product Roadmap?

Learn where Cytoscape has been and what our plans are.

What are 3.x Apps?

Primary documentation for Cytoscape 3.x app development .

All Cytoscape 3.x app development tutorials.

Code for 3.x App Developers

Latest Cytoscape Release:

Quick Start Guides for 2.x App Developers (desupported)
Build Cytoscape 2.x from Source Code (desupported)

GitHub repository is available for all developers. Detailed instruction how to clone 2.x repository is available here. Note that we no longer support this code or repository.

Other Cytoscape 2.x Resources (desupported)

Cytoscape Development Tools

Eclipse is the backbone of our development.

Cytoscape uses YourKit for Java profiling.

All of our projects are build using Maven.
software infrastructure for network biology
Visit the NDEx Project’s website!.