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Software that Uses BioNetGen

This page links to other software that use BioNetGen code or BNGL-formatted models. Note: This list is a work in progress and may not be complete.


Software Description
AMICI Provides an interface to the CVODES and IDAS solvers for models specified in SBML or PySB, both of which are capable of representing BNGL models
BioSimulators Provides a registry of biosimulation tools supporting many different model formats, including BNGL
Kappa Another prominent rule-based modeling language
MCell Uses 3D cellular models and Monte Carlo algorithms for simulating the movements and reactions of molecules within and between cells; the latest version, MCell4, uses BNGL
NFsim Biochemical reaction simulator designed to handle large numbers of possible molecular interactions or states; uses BNGL for model specification
PyBioNetFit Provides a suite of algorithms for parameterizing models specified in BNGL or SBML
PySB Allows for building models of biochemical systems as Python programs; internally translates Python code into BNGL or Kappa rules
RuleDSD Converts a DNA Strand Displacement (DSD) model into BNGL, then uses PySB to perform simulation and analysis
Smoldyn Performs cell-scale biochemical simulations; can perform rule-based modeling using either its native wildcards or by running BioNetGen on BNGL files