Efficient stochastic simulation of reaction-diffusion processes via direct compilation

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

Research output: Contribution to journalArticlepeer-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 languageEnglish
Pages (from-to)2289-2291
Number of pages3
JournalBioinformatics
Volume25
Issue number17
DOIs
StatePublished - 1 Sep 2009
Externally publishedYes

Bibliographical note

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

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