BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. BioNetGen is a software for generating mathematical/computational models that account comprehensively and precisely for the full spectrum of molecular species implied by user-specified activities, potential modifications and interactions of the domains of signaling molecules.
- Windows/ Linux / Mac OsX
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BioNetGen 2.2: Advances in Rule-Based Modeling.
Harris LA, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR.
Bioinformatics. 2016 Jul 8. pii: btw469.
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS.
Bioinformatics. 2004 Nov 22;20(17):3289-91.