Efficient stochastic simulation of reaction-diffusion processes via direct compilation
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Devadas_Efficient stochastic.pdf
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75.31 KB
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Author(s)
Lis, Mieszko
Artyomov, Maxim N.
Chakraborty, Arup K.
Devadas, Srinivas
Date Issued
July 2009
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
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.
MIT 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
Terms of Use
Attribution Non-Commercial License
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/bioinformatics/btp387
