Efficient stochastic simulation of reaction-diffusion processes via direct compilation

Bioinformatics. 2009 Sep 1;25(17):2289-91. doi: 10.1093/bioinformatics/btp387. Epub 2009 Jul 3.

Abstract

We present the Stochastic Simulator Compiler (SSC), a tool for exact stochastic simulations of well-mixed and spatially heterogeneous systems. SSC is the first tool to allow a readable high-level description with spatially heterogeneous simulation algorithms and complex geometries; this permits large systems to be expressed concisely. Meanwhile, direct native-code compilation allows SSC to generate very fast simulations.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Computer Simulation*
  • Diffusion*
  • Stochastic Processes