# Welcome to BioNetGen

BioNetGen provides the user with a system for rule-based modeling of biochemical networks.

The BioNetGen approach addresses the inherent problem of combinatorial complexity within biochemical networks through use of a two stage modeling process. The first stage creates a reaction network through complete specification of the biochemical species involved and the reactions they may undergo. The network is then converted to a corresponding predictive mathematical model consisting of a set of coupled differential equations. The second stage iterates these equations until the allowed reactions achieve a steady state or a user defined stopping point. The user is only involved in the first stage and has complete control over how the reactions in the second stage are allowed to proceed. When the second stage is complete, the output may be exported for plotting in other packages such as Grace for display of timecourse of the observables.

BioNetGen Features
BioNetGen Use Scenarios