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

DucHau Le | Zendy; YungKeun Kwon | Zendy

Open Access

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

Author(s) -

DucHau Le,

YungKeun Kwon

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr466

Subject(s) - plug in , feed forward , robustness (evolution) , computer science , feedback loop , biological network , dynamics (music) , feedback control , control theory (sociology) , artificial intelligence , computational biology , control engineering , biology , control (management) , programming language , engineering , physics , gene , computer security , acoustics , biochemistry

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.

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