Spatial stochastic simulation

StochSS 1.5 Available for Download!

StochSS 1.5 is now officially released!
Version 1.5 includes:

A new model editor: Edit models faster and easier!
Cost analysis functionality: Measure the cost of running jobs in the cloud
Cloud data reproduction: Delete cloud data and reproduce it only when it is needed
Cloud instance type selection: Configure what instance types are used for cloud computation

Details and instructions on how to obtain the code can be found on the Download page
Tutorials are available on the Documentation page
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lötstedt and Andreas Hellander – Uppsala University

StochSS 1.4 available for download!

We are excited to announce the release of StochSS 1.4
Version 1.4 includes spatial stochastic simulation capabilities powered by the PyURDME spatial solver (http://www.pyurdme.org/).
Details and instructions on how to obtain the code can be found on the Download page
Tutorials are available on the Documentation page
Linda Petzold and Chandra Krintz – University of California Santa Barbara
Per Lotstedt and Andreas Hellander – Uppsala Universiteit

PyURDME 1.0 released !

Two members of the StochSS team, Brian Drawert and Andreas Hellander, have just released the first version of their spatial stochastic simulation software called PyURDME.
PyURDME 1.0 is a general software framework for modeling and simulation of stochastic reaction-diffusion processes on unstructured, tetrahedral (3D) and triangular (2D) meshes. Unstructured meshes allow for a more flexible handling of complex geometries compared to structured, Cartesian meshes. The current core simulation algorithm is based on the mesoscopic reaction-diffusion master equation (RDME) model.
We plan to integrate PyURDME into StochSS soon !

Talks at the SIAM conference on Computational Science and Engineering 2013

Several talks related to StochSS were presented at the SIAM conference on Computational Science and Engineering 2013. Some of them have been made available as slides and audio by SIAM:
Linda Petzold: A First Passage Time Algorithm for Reaction-Diffusion Processes on a 2D Lattice.
Andreas Hellander: Efficient Simulation of Mesoscopic Reaction-diffusion Kinetics via Operator Splitting.

URDME 1.2 released

We are happy to announce the release of URDME 1.2. New features include support for Comsol 4.1, 4.2 and 4.3. We have also added the ability to compile the solvers independently of Matlab libraries. This will greatly simplify deployment of URDME jobs by StochSS down the line.
To get URDME 1.2: www.urdme.org
Or visit us on GitHub.
/Andreas

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