BioNetGen

BioNetGen is an open-source software package developed for constructing and simulating rule-based models of complex biological systems. The software tool has been used extensively to model various biological processes, including cell signaling, gene regulation, and metabolism.

One of the key features of BioNetGen is its ability to define only the reactive motifs within macromolecular complexes and the interactions and modifications that involve those motifs instead of manually enumerating all possible species and reactions that can exist within a system. This rule-based modeling approach has proven to be an effective way to address combinatorial complexity in models of biochemical systems.

Models in BioNetGen are written in a human-readable, text-based modeling language known as BNGL or BioNetGen language. Users can add numerous specified actions to a BNGL model file, including generating a reaction network and performing deterministic or stochastic simulations. The software is also designed to export models to different formats, such as SBML and MATLAB language.

One of the most significant advantages of BioNetGen is its ability to interface with NFsim. This "network-free" simulator avoids the enumeration of species and reactions, which may be intractable for large models. Additionally, RuleBender, a visual interface for BioNetGen, provides a user-friendly environment for modeling, including syntax checking/highlighting and visualizations for model debugging and comparison.

BioNetGen is also used as a network generator and simulator in several third-party tools, including the Virtual Cell, BioUML, SRSim, Parts & Pools, pySB, and BioNetFit.