NetDS: A Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks

Abstract

Summary: NetDS is a novel Cytoscape plugin that conveniently simulates dynamics related to robustness, and examines structural properties with respect to feedforward/feedback loops. It can evaluate how robustly a network sustains a stable state against mutations by employing a Boolean network model. In addition, the plugin can examine all feedforward/feedback loops appearing in a network and determine whether or not a pair of loops is coupled. Random networks can also be generated to evaluate whether or not an interesting finding in real biological networks is significantly random. © The Author 2011. Published by Oxford University Press. All rights reserved.