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 (NSM), extended to unstructured meshes by obtaining jump coefficients from the finite element formulation of the corresponding macroscopic equation.
In this manual, we describe how to use the software together with COMSOL Multiphysics 3.4 and Matlab to set up simulations. We provide a detailed account of the code structure and of the available interfaces. This makes modifications and extensions of the code possible. We also give two detailed examples, in which we describe the process of simulating and visualizing two models from the systems biology literature in a step-by-step manner.
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