Multithread hybrid stochastic/deterministic simulation of biochemical reaction networks.



FEATURES

HSimulator is an optimized, multithread 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


HOW TO CITE AND REFERENCES

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.

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.

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.


SUPPORT

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HSimulator
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