bngl

BNGL, short for BioNetGen Language, is a domain-specific language designed for rule-based modeling of biochemical networks. It enables compact representation of molecules with multiple binding sites and state variables, allowing models to capture combinatorial complexity that arises from interactions, modifications, and complex formation.

In BNGL, molecules are defined as agents with named sites that may have internal states (for example, phosphorylated or bound). Bonds connect sites to form complexes, and rules specify how patterns of agents and bonds change over time. Rules can include context and rate constants, enabling concise descriptions of many related reactions without enumerating each one.

A BNGL model includes definitions of molecule types, initial conditions, and parameters. Using the BioNetGen toolset, rules can be used to generate the full reaction network or to drive network-free simulations that operate directly on the rule descriptions. Simulations can be stochastic (Gillespie-type) or deterministic (ODE-like), and outputs typically include time courses and species or complex counts.

BNGL is widely used to model signaling pathways, protein–protein interactions, multi-site phosphorylation, receptor clustering, and other processes where combinatorial diversity is important. It is part of the broader ecosystem of rule-based modeling and is often compared with the Kappa language as an alternative approach.

BNGL models are stored in .bngl text files and are run with BioNetGen or compatible tools such as NFsim. The language and tooling are maintained by researchers in systems biology and have contributed to the study and simulation of complex biochemical networks.