Efficient stochastic simulation of reaction-diffusion processes via direct compilation

Author(s)
Lis, Mieszko; Artyomov, Maxim N.; Chakraborty, Arup K.; Devadas, Srinivas
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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.
Date issued
2009-07
URI
http://hdl.handle.net/1721.1/59816
Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Chemical Engineering; Massachusetts Institute of Technology. Department of Chemistry
Journal
Bioinformatics
Publisher
Oxford University Press
Citation
Lis, Mieszko et al. “Efficient stochastic simulation of reaction–diffusion processes via direct compilation.” Bioinformatics 25.17 (2009): 2289 -2291.
Version: Final published version
ISSN
1460-2059
1367-4803
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