Stochastic reaction-diffusion simulation on unstructured meshes.
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README.md

URDME

Unstructured Reaction-Diffusion Master Equation

www.urdme.org

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

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,

doc/manual.pdf 

System requirements and software dependencies

See the file VERSION for a fuller list.

  • OS, tested with Ubuntu 14.04 LTS, 16.04 LTS, Mac OS X 10.9.5

  • Matlab, tested with versions: 8.4, 9.1

  • Comsol Multiphysics 5.2a with Matlab integration components

  • PDE Toolbox, tested with versions: 1.5, 2.3

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.

  • The software package; B. Drawert, S. Engblom and A. Hellander: "URDME: A modular framework for stochastic simulation of reaction-transport processes in complex geometries", BMC Systems Biology 6(76):1--17 (2012) (doi)

  • The AEM solver; P. Bauer and S. Engblom: "Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics", pp. 519--527 in A. Abdulle, S. Deparis, D. Kressner, F. Nobile and M. Picasso (editors): "Numerical Mathematics and Advanced Applications: ENUMATH 2013", vol 103 of Lecture Notes in Computational Science and Engineering, Springer (2015). (doi)

  • The UDS solver implements the first order method described in S. Engblom: "Computing the Moments of High Dimensional Solutions of the Master Equation" Appl. Math. Comput. 18(2):498--515 (2006). (doi)