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StochSS: an integrated development environment for simulation of biochemical networks

What is being modeled?
Biochemical systems at a wide range of scales
Description & purpose of resource

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.

Spatial scales
whole organism
Temporal scales
10-3 - 1 s
1 - 103 s
weeks to months
This resource is currently
mature and useful in ongoing research
Has this resource been validated?
How has the resource been validated?

Test models, SBML compliance tests

Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)
Which resources?

Biochemical Models

Key publications (e.g. describing or using resource)

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

Linda Petzold
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