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
| 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 |
| BioUML | |
| 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 |
| ML-Rules | |
| ModelingToolkit.jl | |
| NFsim | |
| NFsim | Biochemical reaction simulator designed to handle large numbers of possible molecular interactions or states; uses BNGL for model specification |
| Parts&Pools | |
| 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 |
| SBML_Multi | |
| Smoldyn | Performs cell-scale biochemical simulations; can perform rule-based modeling using either its native wildcards or by running BioNetGen on BNGL files |
| SPATKIN | |
| SRSim | |
| VirtualCell |