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 | References |
|---|---|---|
| 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 | Java platform for -omics data analysis; a BNG plugin allows users to edit rule-based models as either BioUML diagrams or as BNGL text files | |
| Kappa | Another prominent rule-based modeling language. The syntax used to be very similiar to BNGL, but that is less true now. | Boutillier et al. |
| 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 syntax for rule-based modeling | |
| ML-Rules | Multi-level rule-based modeling formalism for modeling biochemical reaction networks | |
| MolClustPy | A Python package to characterize multivalent biomolecular clusters | Chattaraj et al. |
| NFsim | Biochemical reaction simulator designed to handle large numbers of possible molecular interactions or states; uses BNGL for model specification | |
| Parts & Pools | Employs BioNetGen to help design synthetic gene circuits | |
| PEtab | Data format for specifying systems biology parameter estimation problems using SBML | |
| Pleione | Provides methods for parameterizing models written in BNGL or kappa | |
| PyBioNetFit | Provides a suite of algorithms for parameterizing models specified in BNGL or SBML | |
| pyPESTO | Python toolbox for parameter estimation, including options to interface with AMICI and PEtab | |
| PySB | Allows for building models of biochemical systems as Python programs; internally translates Python code into BNGL or Kappa rules | |
| PyViPR | IPython widget for interactively visualizing systems biology models using PySB; supports BNGL and SBML models | |
| 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 | |
| SPATKIN | Uses an extension of BNGL to simluate biomolecular interactions on or at a 2D surface | |
| SRSim | Spatially simulates Brownian Dynamics of rule-based reaction systems (defined in BNGL) in 3D | |
| VDNA-Lab | Employs rule-based modeling (in BNGL format) to simulate DNA assembly systems | |
| VirtualCell | Cell biological systems modeling platform that uses a central database; BioNetGen@VCell can be used to perform rule-based modeling in the platform |