RFC Name : HeadlessModeRFC

Editor(s): Mike Smoot, Allan Kuchinsky

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About this document

This is an official Request for Comment (RFC) for Cytoscape Headless Mode Operation.

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)


"Not yet completely written"

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Cytoscape currently runs only in "window" mode, that is, as a complete, self-contained application. There is a need to access Cytoscape functionality in alternative ways, such as laying out graph images on a webserver or embedding a cytoscape window in a different application.

Biological Questions / Use Cases

  1. A user has hundreds of SIF files that s/he would like to generate images for (say for a web page) without doing so manually via Cytoscape.
  2. A developer would like to provide a Cytoscape network visualization window in his or her application without necessarily providing all of Cytoscape's functionality.
  3. A developer would like to generate network images of graphs from within a separate Java application.
  4. A program or user would like to interact with a single instance of a Cytoscape "server" running in the background without creating a new instance of Cytoscape each time.

General Notes


Deferred Items

Possible Design

Open Issues

Backward Compatibility

Proper support for headless mode would almost certainly imply significant changes to Cytoscape's current command line interface. It would be important to maintain the current options.

Expected growth and plan for growth


Implementation Plan

HeadlessModeRFC (last edited 2009-02-12 01:03:35 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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