Discrete stochastic simulation has become an important and widely-used tool for modeling of biological systems at the molecular scale. At the same time, there is no single place where one can go to develop a discrete stochastic model with increasing levels of complexity: from the early stages, where it may begin as an ODE model, to a well-mixed (spatially homogeneous) discrete stochastic model, to a spatially inhomogeneous stochastic model with complex geometry and multiple internal surfaces, and finally to a spatially inhomogeneous stochastic model where single molecules at a microscopic level may interact with molecules modeled mesoscopically. The focus of the StochSS project is to build such a place: an integrated development environment featuring state of the art algorithms as well as a means for the community to add new algorithms and capabilities, supported on a wide range of hardware from desktop workstations to high-performance clusters in the cloud.
Test models, SBML compliance tests
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist