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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. SimBoolNet is based on an extended Boolean
network model, in which the state of each node is a variable between 0 and
1 representing the probability (or percentage) of activation and each edge
(representing activation or repression) has associated with it a weight
representing efficiency of propagating of the corresponding signal.
References:
Jie Zheng,
David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala and Teresa
M. Przytycka ; SimBoolNet – A Cytoscape Plugin for Dynamic Simulation of
Signaling Networks; Bioinformatics
(submitted)
Zielinski R,
Przytycki PF, Zheng J, Zhang D, Przytycka TM, Capala J; (2009) The
crosstalk between EGF, IGF, and Insulin cell signaling pathways -
computational and experimental analysis. BMC Systems
Biology, 3:88.
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