After more than a year of development, we are happy to announce the release of PyURDME 1.0.0! PyURDME is a Python module for spatial stochastic simulation model development and simulation. PyURDME is connected to URDME in that is uses a modified version of its core solver. While URDME is mainly designed as an interactive Matlab toolbox that makes use of the tight connection between Comsol Multiphysics to provide an interactive modeling environment, PyURDME is an object oriented API relying only on open source software, in particular the FeniCS/Dolfin project, providing great flexibility for modelers and developers to customize computational experiments.
PyURDME has also been designed with Cloud/Distributed computing in mind, and in particular it integrates well with the IPython tools, such as IPython Notebook. We are currently working on a platform for deploying PyURDME as a Cloud appliance, with support for interactive parallel computational experiments via IPython Parallel, so check back soon for updates on this project. We are also working on integration with StochSS, which ill provide an easy-to-use UI assisted endpoint to PyURDME.
PyURDME is a collaboration with Brian Drawert at UCSB.