Cytoscape is generally for visualization of networks. Instead of building
lots of analysis and simulation into Cytoscape, we let users write their own
plugins to do their specific analysis. So whether Cytoscape could be used
as a simulation tool depends on whether a plugin exists to do what you want.
If you've already got a java app that does the simulation you'd like, then
it would probably be best to use that for the simulation and Cytoscape for
the visualization of the results. Yes, Cytoscape can update its view as
state data changes.
Michael Smoot, Ph.D. Bioengineering Department
tel: 858-822-4756 University of California San Diego