swMATH ID: 10400
Software Authors: Drawert, B., Engblom, S.,Hellander, A.
Description: Urdme: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development.
Homepage: http://sourceforge.net/projects/urdme/
Related Software: MesoRD; STEPS; Smoldyn; ReaDDy; Wavos; PySB; StochSS; PhysiCell; Travis CI; pystospa; Python; pybind11; StoSpa2; R; EpiModel; GillespieSSA; amei; GSL; SimInf; CRAN
Cited in: 24 Publications

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