DynNetwork is a OSGi bundle to provide support for importing, visualizing, and analysing dynamical networks in Cytoscape 3. Dynamical networks are imported in form of XGMML files, and the dynamics of nodes, edges, attributes can be visualized at the desired time points. To improve visualization, the nodes can be animated with a dynamic force layout algorithm.
Example of dynamic XGMML files can be found here: <http://code.google.com/p/dynnetwork/downloads/list>
This plugin has been developed in the context of the Google Summer of Code 2012, 2013 and Cytoscape 3 by Sabina Sara Pfister and Jimmy Morzaria under the supervision of John A Brown and Jason Montojo.
DynNetwork now also allows users to compute network parameters/attributes and plot them against time. Detailed documentation for the new features may be found here https://code.google.com/p/dynnetwork/wiki/DynamicGraphMetricsAttributesHelp.
You may find a demo video here