Welcome to PyURDME’s documentation!

PyURDME is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular (2D) meshes. The current core simulation algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) framework.

PyURDME exposes a flexible Python modeling API for model construction and simulation, and the default solver is the NSM core solver from the URDME package. PyURDME depends on the FEniCS finite element software, see http://fenicsproject.org/ and requires GCC for compilation of the core solvers. For a Matlab/Comsol interface, see http://www.urdme.org


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