After the Cytoscape retreat held in San Diego in 2005, it became obvious that Cytoscape needs to support metanodes. A metanode is a graph node that contains a subgraph. It is a mechanism to group nodes in a graph, and it does not concern the criteria followed to determine membership of a group. There are many different ways of modeling and visualizing metanodes, depending on the biological application in question.

The objectives of the metanodes group is to:

This RFC is a forum for discussing each one of these objectives.

Iliana Avila developed a Cytoscape plugin that implements one possible way of modeling and visualizing metanodes. This plugin can be used as a concept plugin, so that everyone involved has a clearer idea of what is a metanode, and how it can be used. It is by no means the final implementation of metanodes. See "Concept Plugin" section in this Wiki to learn how to obtain and use the plugin.

Comment summary

Biological Applications and their MetaNode Needs

Please add your biological application, and a possible metanode solution.

1. Biomodules

2. Protein Complexes - Pico/GenMAPP (note by Cline/Pasteur)

3. Intragenic Features - Pico/GenMAPP

4. Boxing of groups.

Comment biological applications

Implementation Strategy


Look here SimplifiedMetaNodeDataStructureRFC to learn about how this implementation could be affected in the future.

General Strategy

The strategy will be to add to Cytoscape metanode support in the form of a core plugin and a core library for the 2.3 release. This will allow users to do the following:

For 2.4, we will more fully integrate metanodes with the Cytoscape core. This entails making the core aware of metanodes (for example, when the users searches for a node by its name, the core should not only search visible nodes in a network, but also non-visible children nodes of metanodes). For 2.4, other core plugins (like the editor, the attributes browser, and filters) should also be made aware of the existence of metanodes.

Comment general strategy

Specific Action Items for Each Release

Cytoscape 2.3

Other possible items are:

Comment 2.3 action items

Cytoscape 2.4

No defined specific action items yet

Concept Plugin


Login anonymously into CVS and checkout csplugins:

  1. cvs -d login

  2. cvs -d co csplugins

  3. cvs -d logout

The plugin is located in: /csplugins/isb/iavila/metaNodeViewer. Edit the build.xml file if necessary to point to the correct Cytoscape path (works with latest Cytoscape version). Type: ant run. The plugin is available in the plugins menu, and as a right click context menu (which seems to not appear sometimes...)


MetaNodes_RFC (last edited 2009-02-12 01:03:02 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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