Journal Article

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

Duc-Hau Le and Yung-Keun Kwon

in Bioinformatics

Volume 27, issue 19, pages 2767-2768
Published in print October 2011 | ISSN: 1367-4803
Published online August 2011 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btr466
NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks

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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: kwonyk@ulsan.ac.kr

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1544 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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