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Bioinformatics Advance Access published online on November 3, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp617
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SimBoolNet - A Cytoscape Plugin for Dynamic Simulation of Signaling Networks

Jie Zheng 1,*, David Zhang 4, Pawel F. Przytycki 3, Rafal Zielinski 2, Jacek Capala 2 and Teresa M. Przytycka 1,*

1National Center for Biotechnology Information, NLM/NIH, Bethesda, MD
2National Cancer Institute, NIH, Bethesda, MD
3Columbia University, Columbia College, New York, NY
4Department of Electrical & Computer Engineering, University of Maryland, College Park, MD

*To whom correspondence should be addressed. Jie Zheng, Teresa M. Przytycka, E-mail: zhengj{at}ncbi.nlm.nih.gov, przytyck{at}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

Contact: przytyck{at}ncbi.nlm.nih.gov or zhengj{at}ncbi.nlm.nih.gov

Associate Editor: Dr. Jonathan Wren

Received on July 25, 2009; revised on October 23, 2009; accepted on October 25, 2009

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