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Stochastic reaction-diffusion simulation on unstructured meshes.


Unstructured Reaction-Diffusion Master Equation

URDME is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on arbitrary meshes. URDME emphasizes modularity in order to be useful both as a simulation tool and as a framework for development of stochastic simulation algorithms.

URDME 1.3. Copyright 2008–2017

See the file AUTHORS for a complete list of authors.

Quick Start

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

$ git clone

To start using URDME under Matlab, navigate to the file startup.m,

>> startup

To run a simple 1D model,

>> cd examples/annihilation
>> annihilation_run

For further instructions, examples and tutorials, consult the software manual,


System requirements and software dependencies

See the file VERSION for a fuller list.

Licence: GPL 3

See the file LICENCE for the full statement.

Citing URDME:

URDME is a research software and correctly citing it is important to the maintainers.