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, R. Lombardo, C. Priami. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks, Complexity, Volume 2017, Article ID 1232868, DOI: 10.1155/2017/1232868, 2017.
L. Marchetti, C. Priami, V. H. Thanh. Simulation Algorithms for Computational Systems Biology. Springer International Publishing, Berlin, Germany, 2017.
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.
Please address all enquiries about HSimulator to the HSimulator Team