Efficient stochastic simulation of reaction-diffusion processes via direct compilation.
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ABSTRACT:
SUBMITTER: Lis M
PROVIDER: S-EPMC2734316 | biostudies-literature | 2009 Sep
REPOSITORIES: biostudies-literature
Publications
Efficient stochastic simulation of reaction-diffusion processes via direct compilation.
Lis Mieszko M Artyomov Maxim N MN Devadas Srinivas S Chakraborty Arup K AK
Bioinformatics (Oxford, England) 20090703 17
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. ...[more]
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