HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Luca Marchetti, Rosario Lombardo and Corrado Priami

Complexity, 2017, vol. 2017, 1-12

Abstract:

HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA).

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:hin:complx:1232868

DOI: 10.1155/2017/1232868

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