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.
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
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.
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.
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)