Bioinformatics. 2010 Jan 1;26(1):141-2. Epub 2009 Nov 3.

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks.

Zheng J, Zhang D, Przytycki PF, Zielinski R, Capala J, Przytycka TM.

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National Center for Biotechnology Information, NLM/NIH, Bethesda, MD, USA. zhengj@ncbi.nlm.nih.gov

Abstract

SUMMARY: SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways. AVAILABILITY: SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet

PMID:: 19887508; [PubMed - indexed for MEDLINE]
PMCID:: PMC2796819

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