In cases for which mean-field analysis has been shown to be insufficient, stochastic models provide a more accurate, yet computationally tractable alternative. Stochastic simulation of reaction kinetics has emerged as an important computational tool in molecular systems biology. 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. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency.
An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. 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. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation.
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