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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

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 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
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
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
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
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
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
VirtualCell Cell biological systems modeling platform that uses a central database; BioNetGen@VCell can be used to perform rule-based modeling in the platform