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.
/Andreas

Welcome to StochSS

Welcome to the StochSS site! StochSS (Stochastic Simulation as a Service)
is our NIBIB-funded project to make discrete stochastic simulation easy and accessable. In the first version of StochSS we are focusing on simulation capabilities for cell biology. Our goal is to enable you to build a model (or models), scale it up to increasing complexity including incorporating spatial dependence, characterization or rare events, and parameter estimation, and explore the parameter space.
StochSS will be available on your desktop as a web app. As your computational needs grow, StochSS will be able to seamlessly deploy the appropriate computing resources as needed, via cloud computing. The foundation of the cloud computing capabilities is the AppScale open source cloud platform, developed by the Krintz group at UCSB. Appscale can link to a variety of commercial clouds, or you can turn your local cluster into a cloud.
Stay tuned for StochSS v1.0, coming soon!
The StochSS team
Linda Petzold, Chandra Krintz, Andreas Hellander, Per Lötstedt, Ben Bales, Bernie Daigle, Sheng Wu, Jin Fu, Chris Bunch, Brian Drawert, Hiranya Jayathilaka, Stefan Hellander