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URDME

Stochastic reaction-diffusion simulation on unstructured meshes.

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Welcome to the URDME Webpage.

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.

Quick Start

Download the latest stable release and unpack it, alternatively clone the repository (requires a git client). In a terminal type:

$ git clone https://github.com/URDME/urdme.git
$ sudo ./install.sh

Consult the software manual in doc/manual.pdf for further instructions, examples and tutorials.

System requirements and software dependencies

Copyright

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

Publications

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

Acknowledgments

This work was financially supported by the Swedish Research Council within the UPMARC Linnaeus center of Excellence.

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