ChemCell WWW Site

ChemCell Features

ChemCell is a particle-based reaction/diffusion simulator designed to model signaling, regulatory, or metabolic networks in biological cells. It can be run as a spatial simulator where the particles diffuse within the specified geometry of a cell, or as a non-spatial simulator where there is no diffusion and the network of chemical reactions is time-integrated as a set of ODEs or stochastically via the Gillespie Stochastic Simulation Algorithm (SSA).

For spatial simulations, a single protein, protein complex, or other biomolecule is represented as a dimensionless particle. The geometry of a cell (membranes, organelles, etc) is represented as simple geometrical objects (spheres, boxes, etc) or as triangulated surfaces. Particles diffuse randomly via Brownian motion, either in 3d or on 2d surfaces. Biochemical reactions occur in accord with chemical rate equations, which are inputs to ChemCell. Monte Carlo rules are used to perform reactions each timestep between pairs of nearby particles.

For non-spatial simulations, the cell is treated as a well-mixed chemical reactor, and the chemical rate equations can be time-integrated either by a fixed-step or adaptive-timestep ODE solver or by the direct-method variant of the Gillespie Stochastic Simulation Algorithm (SSA) using the Gibson/Bruck methodology.

ChemCell runs on single-processor desktop or laptop machines, but can also be run in parallel. Multiple runs can be performed on a collection of processors (for statistical purposes), or (for spatial simulations) the simulation domain can be partitioned across processors and a single simulation run in parallel. For spatial simulations, ChemCell can model systems with only a few particles up to many millions.

ChemCell is a freely-available open-source code, distributed under the terms of the GNU Public License, which means you can use or modify the code however you wish. See this page for a brief discussion of the open-source philosophy.

ChemCell is designed to be easy to modify or extend with new capabilities, such as modified reaction rules or boundary conditions. See this section for more details.

ChemCell is written in C++ and can be downloaded from the ChemCell WWW Site. No additional software is needed to run ChemCell in serial on a desktop machine. ChemCell will run on any parallel machine that compiles C++ and supports the MPI message-passing library. This includes distributed- or shared-memory parallel machines and Beowulf-style clusters. To run with spatial parallelism, the Zoltan library must also be installed.

ChemCell does not have the ability to create cellular geometries or visualize simulation output. Currently, these tasks are handled by pre- and post-processing codes. Our group has written a separate toolkit called which provides tools for doing setup, analysis, plotting, and visualization for ChemCell simulations. is written in Python and is available for download from the WWW site.

More details about ChemCell are given in the ChemCell documentation.