HSimulator: Hybrid StochasticDeterministic Simulation of Biochemical Reaction Networks

Abstract EN

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).