Efficient stochastic simulation of reaction-diffusion processes via direct compilation

Mieszko Lis; Maxim N. Artyomov; Srinivas Devadas; Arup K. Chakraborty

doi:10.1093/bioinformatics/btp387

Efficient stochastic simulation of reaction-diffusion processes via direct compilation

Mieszko Lis
, Maxim N. Artyomov
, Srinivas Devadas
, Arup K. Chakraborty

Massachusetts Institute of Technology

Research output: Contribution to journal › Article › peer-review

53 Scopus citations

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.

Original language	English
Pages (from-to)	2289-2291
Number of pages	3
Journal	Bioinformatics
Volume	25
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btp387
State	Published - 1 Sep 2009
Externally published	Yes

Bibliographical note

Funding Information:
This research was funded by NIH Grant #1PO1/AI071195/01.

Funding

This research was funded by NIH Grant #1PO1/AI071195/01.

Funders	Funder number
National Institutes of Health
National Institute of Allergy and Infectious Diseases	P01AI071195

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10.1093/bioinformatics/btp387

Cite this

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Efficient stochastic simulation of reaction-diffusion processes via direct compilation

Abstract

Bibliographical note

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