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,
A BNGL model includes definitions of molecule types, initial conditions, and parameters. Using the BioNetGen toolset,
BNGL is widely used to model signaling pathways, protein–protein interactions, multi-site phosphorylation, receptor clustering, and other
BNGL models are stored in .bngl text files and are run with BioNetGen or compatible tools such