ChemCell WWW Site - ChemCell Documentation - ChemCell Commands

ChemCell Documentation

Version info:

The ChemCell "version" is the date when it was released, such as 1 May 2010. ChemCell is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of ChemCell contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run ChemCell. It is also in the file src/version.h and in the ChemCell directory name created when you unpack a tarball.

ChemCell is a particle-based reaction/diffusion simulator designed for modeling protein networks in biological cells with spatial information. Compartments within the cell are bounded by membrane surfaces defined as geometric regions or connected triangles. Particles represent individual biomolecules and diffuse via Brownian motion in 3d and on 2d surfaces. Particles react with neighboring particles according to rules derived from chemical rate equations. Non-spatial models can also be run using an ODE solver or the Gillespie Stochastic Simulation Algorithm (SSA). Spatial simulations can be run in parallel as can multiple instances of non-spatial simluations for statistical averaging. The Pizza.py package of Python-based tools can create input files for ChemCell and visualize and plot its output.

ChemCell was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, designed to be easy to modify and extend with new functionality. It is distributed freely under the terms of the GNU Public License (GPL).

The authors of the code are Steve Plimpton and Alex Slepoy, who can be contacted at sjplimp at sandia.gov and alexander.sleopy at nnsa.doe.gov. The ChemCell WWW Site at http://chemcell.sandia.gov has more information about the code and its uses.


The ChemCell documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send us mail so we can improve the ChemCell documentation.

PDF file of the entire manual, generated by htmldoc

  1. Introduction
  2. Getting started
  3. Commands
  4. Example problems
  5. Additional tools
  6. Modifying & Extending ChemCell
  7. Errors