Hi all
Found a new interesting free software
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.
Guy

Hi Guy,

Ya Cytoscape is great. Its used to generate the majority of those giant graphs you see of things like protein-protein interaction networks. Its also used by this student's SNP related workflow.

Not to mention is was selected as the best tool for visualizing graphs in a recent survey by a key semantic web blogger / guru. http://www.mkbergman.com/?p=415.