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.
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.
-
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