Extending URDME

The first version of StochSS will support well mixed stochastic simulation using solvers from StochKit2 , but the work to incorporate spatial stochastic solvers are starting already now. For the spatial solvers, we will use algorithms from URDME as a computational backend. URDME is a modular framwork with a Matlab frontend, and uses Comsol Multiphysics to define and construct the spatial components of the model. Currently, its main use is as an interactive environment functioning much as a Matlab toolbox. Models are specified using a Matlab/Comsol API.
To make the solvers of URDME readily available to StochSS we are currently working on extending URDME to support open-source software for geometry modelling and meshing, and on a Python API for model specification. This Python interface will also be made available as an alternative frontend to URDME.