Uppsala University Department of Information Technology

Technical Report 2012-036

URDME v. 1.2: User's manual

Pavol Bauer, Brian Drawert, Stefan Engblom, and Andreas Hellander

December 2012

We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations on structured, cartesian meshes. The underlying algorithm is the next subvolume method, extended to unstructured meshes by obtaining jump coefficients from a finite element formulation of the corresponding macroscopic equation. This manual describes version 1.2 of the software. URDME 1.2 includes support for Comsol Multiphysics 4.1, 4.2, 4.3 as well as the previous version 3.5a. Additionally, support for basic SBML has been added along with the possibility to compile in stand-alone mode.

Note: Also available at http://arxiv.org/abs/0902.2912

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Uppsala Universitet