Simulators

• CPCMP
  GPGMP is a very fast implementation of a spatially-resolved reaction advection diffusion simulation algorithm on general-purpose graphics processing units. You can use GMGMP either in a complete simulation environment with a graphical user interface, called Inchman. The basic system is described in Vigelius, M., Lane, A. and Meyer, B. (2010). Accelerating Reaction-Diffusion Simulations with General-Purpose Graphics Processing Units. Bioinformatics (2010), First published online:
  November 8, 2010, doi: 10.1093/bioinformatics/btq622.You can find complete information on GPGMP and inchman at http://www.csse.monash.edu.au/~berndm/inchman/
• Lattice Microbes
  Lattice Microbes implements the Reaction Diffusion Master Equation (RDME) using GPUs for enhance computational speed. Models are created using a python interface.
• MCell
  MCell (Monte Carlo cell) is a program that uses spatially realistic 3-D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells—cellular microphysiology.
• MEDYAN
  MEDYAN is a hybrid cytoskeletal simulation package which combines the reaction-diffusion of cytosolic species with complex polymer chain mechanics to fully simulate cytoskeleton and its constituent filament mechanochemistry. It uses a Reaction Diffusion Master Equation approach to generate stochastic trajectories of complex cytoskeletal network evolution ranging from contractile actomyosin networks to dendritically branched actin networks. The package is available for download and contains documentation and examples for running the code as well as visualizing and analyzing its output.
• NeuroRD
  NeuroRD is a meso-scopic simulator of reaction diffusion systems, designed for simulator signaling pathways in neuronal dendrites and spines, with an easy to learn xml model specification. The morphology is subdivided into a lattice/mesh, either using cubes or curved elements. The simulation algorithm employs tau-leaping for both reactions and diffusion, and thus is computationally efficient for high molecule densities. NeuroRD is implemented in java, and thus runs on any OS. It has an easy-to-use xml interface, with several tutorials and examples provided. Version 3, which presents an asynchronous tau-leaping algorithm, has just been released.
• ReaDDy
  ReaDDY is an open source Java Library for simulating particle based Reaction Diffusion systems. It is written in java, and runs on Windows, Linux, Mac, with Java Version 6 or later. By incorporating particle interaction potentials, the algorithm permits simulating effects such as space exclusion and molecular crowding.
• Smoldyn
  Smoldyn is a simulator for modeling cell biology processes with spatial and stochastic detail. It represents molecules of interest as individual spherical particles that have continuous-valued spatial locations (i.e. not lattice). It represents membranes and other surfaces using constructive geometry, in which the modeler defines them from spheres, cylinders, triangles, and other geometric primitives. Simulation time steps have a fixed length, which results in efficient but approximate simulations. During a simulation, molecules diffuse, undergo chemical reactions, and interact with surfaces, much as they do in a real biochemical system. All of these rates have been shown to be accurate to within 2.5%, by comparison against exact results. Smoldyn can conveniently simulate up to hundreds of thousands of molecules over several minutes of real time. It is open source, runs on Macs, Windows, and Linux, comes with a complete user’s manual, and is easy to use.
• STEPS
  STEPS a GPL3.0 licensed package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie’s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. STEPS is implemented in C/C++, with Python as its user interface.
• StochSS
  StochSS provides an integrated development environment for stochastic simulations of biochemical networks and population systems.
• URDME
  URDME is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral and triangular meshes. URDME emphasizes modularity in order to be useful both as a simulation tool and as a framework for development of stochastic simulation algorithms. The framework consists of several core solvers written in C which are accessible over a MATLAB interface, or python interface. Spatial models can be imported using Comsol Multiphysics.