Cytoscape

(from http://www.cytoscape.org/features.phpwww.cytoscape.org):
Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.

An additional feature could be visualizing the simulation of a reaction network. This is provided by the FERN cytoscape plugin (for more information about FERN please refer to the FERN documentation available at /fern/fern).