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| Amici - A multi-language interface to the SUNDIALS solvers CVODES and IDAS. |
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| Berkeley Madonna - General purpose differential equations solver with GUI for constructing complex mathematical models. |
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| BioDynaMo - Platform for 3D agent-based simulations. |
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| BioNetGen/RuleBender - Rule-based dynamical modeling; RuleBender is a GUI interface for BioNetGen. |
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| BioSimulations - is a free platform for sharing and re-using biomodels, simulations, and visualizations. |
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| BioSimulators - is a free platform for sharing and re-using biomodels, simulations, and visualizations. |
| BoolNet - R package for the construction and analysis of synchronous, asynchronous, probabilistic and temporal Boolean networks. |
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| Cell Collective - Web-based platform for the construction, simulation, and analysis of Boolean-based models. |
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| Cell Designer - A structured diagram editor for drawing gene-regulatory and biochemical networks stored in SBKL. |
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| CellNetAnalyzer - MATLAB toolbox for exploring structural and functional properties of metabolic, signaling, and regulatory networks using stoichiometric and constraint-based techniques as well as Boolean and multivalued logic. |
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| CellNOpt - Creates logic-based models of signal transduction networks using different logic formalisms (Boolean, Fuzzy, or differential equations). Encodes information on signaling pathways as a Prior Knowledge Network, and trains it against high-throughput biochemical data to create cell-specific models. |
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| CNApy - A cross-platform desktop application written in Python for constraint-based analysis of metabolic networks. |
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| CobraPy - Python package that provides a simple interface to metabolic constraint-based reconstruction and analysis. |
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| CompuCell3D - CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations. |
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| CoMSES - Compilation of software for agent- based modeling. |
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| COPASI - Nonspatial deterministic and stochastic, parameter optimization and steady state analysis. |
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| Cytoscape - is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. |
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| E-Cell System - A platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems. |
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| Escher-FBA - An interactive pathway visualization tool for on-the-fly flux balance analysis (FBA) calculations. |
| GFRD - Algorithm for single particle reaction diffusion systems using Green's Function. |
| GillesPy2 - Python package for stochastic simulation of biochemical systems. |
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| GINsim - Specifies a model of a genetic regulatory network in terms of asynchronous, multivalued logical functions, and simulates and/or analyses its qualitative dynamical behavior. |
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| Ibiosim - Modeling, analysis, and design of genetic circuits |
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| JWSonline - Tool for the construction, modification and simulation of kinetic models and for the storage of curated models. |
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| MaBoSS - Markovian Boolean Stochastic Simulator for simulating continuous/discrete time Markov processes based on Boolean networkss based on Boolean networks. |
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| MCell - Monte Carlo spatial stochastic reaction diffusion simulator |
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| modelbase - Python package for building and analyzing dynamic mathematical models originally designed for simulating metabolic systems. |
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| Morpheus - Modeling and simulation environment for the study of multi-scale and multicellular systems using ODEs, PDEs and cellular Potts models. |
| NERDSS - NonEquilibrium Reaction-Diffusion Self-assembly Simulator |
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| Neuron - Environment for building and using computational models of neurons and networks of neurons. |
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| OpenCOR - An open source cross-platform modelling environment |
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| PySCeS - A collection of Python-based tools for the analysis of cellular systems. |
| Simmune - Spatial modeling of cell biological systems from interactions between molecular domains to the behavior of populations of cells |
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| Smoldyn - Spatial Stochastic simulator for chemical reaction networks. |
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| Spatiocyte - Lattice-based particle simulator |
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| SpringSaLaD - Particle-based, stochastic, biochemical simulation platform for meso-scale modeling that explicitly accounts for individual domains within a protein. |
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| StochSS - Web interface for simulating stochastic and ODE-based biochemical systems. |
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| Tellurium - Python-based modeling environment for systems and synthetic biology. |
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| VCell - Spatial and nonspatial deterministic, stochastic, hybrid stochastic/deterministic simulations with GUI and central database and computing services |
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| Vivarium-Collective - a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism. |
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