Multithread hybrid stochastic/deterministic simulation of biochemical reaction networks. HSimulator is an optimized, multi-threaded Java simulator compatible with Java 6.0 or higher versions. The simulator works both in terminal and in a graphical environment thanks to an ad hoc GUI. HSimulator is also a Javadoc documented Java library, which can be linked to any Java application to provide simulation facilities. The software provides an efficient implementation of five simulation algorithms: DM: the Direct Method introduced by Gillespie; RSSA: an exact and efficient simulation algorithm for large-scale biochemical reactions; Euler: the forward Euler deterministic simulation algorithm; RK45: the Runge-Kutta-Fehlberg deterministic algorithm; HRSSA: a novel hybrid stochastic/deterministic simulation algorithm, which allows fast and accurate simulations.
HSimulator
R. Lombardo;C. Priami
2017-01-01
Abstract
Multithread hybrid stochastic/deterministic simulation of biochemical reaction networks. HSimulator is an optimized, multi-threaded Java simulator compatible with Java 6.0 or higher versions. The simulator works both in terminal and in a graphical environment thanks to an ad hoc GUI. HSimulator is also a Javadoc documented Java library, which can be linked to any Java application to provide simulation facilities. The software provides an efficient implementation of five simulation algorithms: DM: the Direct Method introduced by Gillespie; RSSA: an exact and efficient simulation algorithm for large-scale biochemical reactions; Euler: the forward Euler deterministic simulation algorithm; RK45: the Runge-Kutta-Fehlberg deterministic algorithm; HRSSA: a novel hybrid stochastic/deterministic simulation algorithm, which allows fast and accurate simulations.
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