PyURDME is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular (2D) meshes. Unstructured meshes allow for a more flexible handling of complex geometries compared to structured, Cartesian meshes. The current core simulation algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) model. PyURDME was originally based on the URDME software package, but has been completely rewritten in python and updated. It depends on the FEniCS libraries for mesh generation and assembly, see The core simulation routines are implemented in C, and requires GCC for compilation. The default solver is an efficient implementation of the Next Subvolume Method (NSM).

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References in zbMATH (referenced in 2 articles )

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  1. MacNamara, Shev; Henry, Bruce; McLean, William: Fractional Euler limits and their applications (2017)
  2. Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas: MOLNs: a cloud platform for interactive, reproducible, and scalable spatial stochastic computational experiments in systems biology using pyurdme (2016) ioport