The Stochastic Simulation Compiler

The Stochastic Simulation Compiler (SSC) is a tool for creating exact stochastic simulations of biochemical reaction networks. The models are written in a succinct, intuitive format, where reactions are specified with patterns. Patterns mention only the part of the compound relevant to a given reaction, and correspond to an intuitive view of biochemical reactions. This enables complex biochemical signaling networks to be specified without the knowledge of any formal programming languages.

Models created using SSC can consist of separate regions in which reactions and diffusions take place, making it easy to model systems with, e.g., several cellular compartments separated by membranes. Arbitrarily complex container shapes can be specified using Constructive Solid Geometry (CSG).

SSC compiles the model into fast simulators. Part of the speedup comes from algorithmic improvements to the original Gillespie algorithm, while the rest comes from directly generating efficient native code.



SSC 0.6:

SSC 3D Viewer:

You may be asked to grant the viewer unrestricted access to your computer (because it needs to open trajectory files and save movies on your computer, and because it requires access to your graphics card to display 3D). Some versions of Internet Explorer require you to download the link to your desktop and double-click to start the viewer.

SSC trajectory reader:

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