Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan 1;26(1):141-2.
doi: 10.1093/bioinformatics/btp617. Epub 2009 Nov 3.

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

Jie Zheng  1 , David Zhang, Pawel F Przytycki, Rafal Zielinski, Jacek Capala, Teresa M Przytycka
Affiliations

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

Jie Zheng et al. Bioinformatics. .

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

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Screenshots of SimBoolNet. The top is the result of a single-mode simulation, where red color represents high percentage of phosphorylation. The bottom-left is a chart visualizing the changes of node activities with time. The bottom-right is a scatter plot and regression line between a signal receptor and a down-stream node from a batch simulation.
See this image and copyright information in PMC

References

    1. Albert I. Boolean network simulations for life scientists. Source Code Biol. Med. 2008;3:16. - PMC - PubMed
    1. Aldridge BB, et al. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput. Biol. 2009;5:e1000340. - PMC - PubMed
    1. Gilbert D. The JFreeChart Class Library. 2009 Available: http://www.jfree.org/jfreechart/ (last accessed date September 18, 2009)
    1. Gilbert D, et al. Computational methodologies for modelling, analysis and simulation of signalling networks. Brief. Bioinform. 2006;7:339–353. - PubMed
    1. Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–2504. - PMC - PubMed

Publication types