The PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/
