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Stochastic reaction-diffusion simulation on unstructured meshes.

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urdme

URDME 1.2. Copyright 2008,2009,2010,2011,2012. See the file AUTHORS for complete list of authors.

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 developemnt of stochastic simulation algorithms.

www.urdme.org

Quick Start

Download the latest stable release and unpack it, alternatively clone the repository (requires a git client)

-- In a terminal --

$ git clone https://github.com/URDME/urdme.git

$ sudo ./install.sh

Consult the software manual:

  • doc/manual.pdf

for further instructions, examples and tutorials.

System requirements and software dependencies

  • Linux or Apple OSX operating system.

  • Matlab -Tested versions: 2007a, 2008a, 2008b, 2009a, 2009b, 2011b, 2012a. Command line interface must be installed.

  • Comsol multiphysics 3.5a (with appropriate patches) or Comsol multiphysics 4.x -Tested versions: 3.5a, 4.0, 4.2, 4.3 (recommended)

    • Must have Matlab integration components installed
  • GCC (Xcode on Apple computers+command-line tools)

    • Executables gcc and make must be in the path
    • Standard libraries must be installed
  • The optional SBML support requires additionally

    • Python runtime libraries 2.6 or higher
    • SBML library for python (libsbml)

Additional information can be found in the paper:

  • URDME: A modular framework for stochastic simulation of reaction-transport processes in complex geometries, B. Drawert, S. Engblom and A. Hellander, BMC Systems Biology 2012 6:76

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