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


BACKGROUND
SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet
Zheng
Jie
J
National Center for Biotechnology Information, NLM/NIH, Bethesda, MD, USA. zhengj@ncbi.nlm.nih.gov
Zhang
David
D
Przytycki
Pawel F
PF
Zielinski
Rafal
R
Capala
Jacek
J
Przytycka
Teresa M
TM
D000465:Algorithms; D003198:Computer Simulation; D008954:Models, Biological; D015233:Models, Statistical; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D020543:Proteome