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Complexity
Volume 2017 (2017), Article ID 1232868, 12 pages
https://doi.org/10.1155/2017/1232868
Research Article

HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

1The Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy
2Department of Computer Science, University of Pisa, Pisa, Italy

Correspondence should be addressed to Luca Marchetti

Received 12 May 2017; Revised 18 August 2017; Accepted 19 November 2017; Published 13 December 2017

Academic Editor: Valeri Mladenov

Copyright © 2017 Luca Marchetti et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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).