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

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. AVAILABILITY NetDS is freely available for non-commercial purposes at http://netds.sourceforge.net/. CONTACT [email protected] SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.