Abstract
We present StochSS: Stochastic Simulation as a Service, an integrated development environment for modeling and simulation of both deterministic and discrete stochastic biochemical systems in up to three dimensions. An easy to use graphical user interface enables researchers to quickly develop and simulate a biological model on a desktop or laptop, which can then be expanded to incorporate increasing levels of complexity. StochSS features state-of-the-art simulation engines. As the demand for computational power increases, StochSS can seamlessly scale computing resources in the cloud. In addition, StochSS can be deployed as a multi-user software environment where collaborators share computational resources and exchange models via a public model repository. We demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.
Highlights
A striking outcome of the past decade of Systems Biology research is the insight that stochasticity plays an important role in many biological processes
We have addressed these issues in StochSS, first by providing an integrated development environment powered by an easy-to-use web-based user interface (WebUI) that allows model transition from the simplest ordinary differential equation (ODE) models to the most complex spatial stochastic models, backed by native 2D and 3D visualization for smooth model debugging and presentation, and second by making it simple to scale computational resources as the problem size grows without the need to integrate with complicated distributed systems
StochSS features a collection of tools designed for the modeling and simulation of well-mixed chemically reacting models, discrete stochastic models, and spatial stochastic models, exposed to the user through a simple, powerful, cross-platform WebUI
Summary
A striking outcome of the past decade of Systems Biology research is the insight that stochasticity plays an important role in many biological processes. The amount of computational power needed for conducting large-scale computational experiments calls for distributed computing on clusters, grids or clouds, which requires a level of computer science expertise not possessed by most biologists We have addressed these issues in StochSS, first by providing an integrated development environment powered by an easy-to-use web-based user interface (WebUI) that allows model transition from the simplest ODE models to the most complex spatial stochastic models, backed by native 2D and 3D visualization for smooth model debugging and presentation, and second by making it simple to scale computational resources as the problem size grows without the need to integrate with complicated distributed systems. This feature makes StochSS a powerful tool for educational efforts in quantitative modeling, since it enables use of StochSS on popular and cheap clients
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