Old News

See our new Rule-Based Modeling Community for more information about this growing field. If you are already working in this area, we welcome your addition the the Community page(s).
See the newly-added Tips section below.
RuleBender is an integrated development environment for BioNetGen that provides a self-contained and easy-to-use interface for model development, simulation, and analysis. An Applications Note describing RuleBender has been accepted to Bioinformatics.
NFsim is a new simulator for rule-based models that supports agent-based simulation and coarse-graining of reactions, which greatly extends the range of models that can be specified and simulated in the BioNetGen language. See also a paper describing NFsim that just appeared in Nature Methods. Support for global and local functions using ODE and SSA methods will be provided starting in release 2.1.8 of BioNetGen.
See our new Rule-Based Modeling Primer for a gentle introduction to rule-based modeling with BioNetGen.
The BioNetGen to Stochastic Simulation Compiler (SSC) translator is a new feature of BioNetGen introduced in release 2.1.6. SSC is a tool for creating spatially resolved, exact stochastic simulations of biochemical reaction networks. The translator can automatically convert BioNetGen models to SSC models. Click here for more information.