Efficient stochastic simulation of reaction–diffusion processes via direct compilation

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 larg...

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Detalles Bibliográficos
Autores principales: Lis, Mieszko, Artyomov, Maxim N., Devadas, Srinivas, Chakraborty, Arup K.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734316/
https://www.ncbi.nlm.nih.gov/pubmed/19578038
http://dx.doi.org/10.1093/bioinformatics/btp387
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author Lis, Mieszko
Artyomov, Maxim N.
Devadas, Srinivas
Chakraborty, Arup K.
author_facet Lis, Mieszko
Artyomov, Maxim N.
Devadas, Srinivas
Chakraborty, Arup K.
author_sort Lis, Mieszko
collection PubMed
description 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. Availability: SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/. Contact: mieszko@csail.mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-27343162009-08-31 Efficient stochastic simulation of reaction–diffusion processes via direct compilation Lis, Mieszko Artyomov, Maxim N. Devadas, Srinivas Chakraborty, Arup K. Bioinformatics Applications Note 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. Availability: SSC currently runs on Linux and Mac OS X, and is freely available at http://web.mit.edu/irc/ssc/. Contact: mieszko@csail.mit.edu Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2009-09-01 2009-07-03 /pmc/articles/PMC2734316/ /pubmed/19578038 http://dx.doi.org/10.1093/bioinformatics/btp387 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Lis, Mieszko
Artyomov, Maxim N.
Devadas, Srinivas
Chakraborty, Arup K.
Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title_full Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title_fullStr Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title_full_unstemmed Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title_short Efficient stochastic simulation of reaction–diffusion processes via direct compilation
title_sort efficient stochastic simulation of reaction–diffusion processes via direct compilation
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734316/
https://www.ncbi.nlm.nih.gov/pubmed/19578038
http://dx.doi.org/10.1093/bioinformatics/btp387
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AT devadassrinivas efficientstochasticsimulationofreactiondiffusionprocessesviadirectcompilation
AT chakrabortyarupk efficientstochasticsimulationofreactiondiffusionprocessesviadirectcompilation

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