HSimulator

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

 

References

L. Marchetti, R. Lombardo, C. Priami. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks, Complexity, Volume 2017, 2017. link

L. Marchetti, C. Priami, V. H. Thanh. Simulation Algorithms for Computational Systems Biology. Springer International Publishing, Berlin, Germany, 2017. link

L. Marchetti, C. Priami, V. H. Thanh. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks, J. Comp. Phys., 317:301–317, 2016. link

V. H. Thanh, C. Priami and R. Zunino. Efficient Rejection-based Simulation of Biochemical Reactions with Stochastic Noise and Delays, J. Chem. Phys., 141(13):134116, 2014. link

V. H. Thanh, R. Zunino and C. Priami. On the Rejection-based Algorithm for Simulation and Analysis of Large-Scaled Reaction Networks, J. Chem. Phys., 142(24):244106, 2015. link