Calendar queues: a fast 0(1) priority queue implementation for the simulation event set problem
Communications of the ACM
Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator
ACM Transactions on Modeling and Computer Simulation (TOMACS) - Special issue on uniform random number generation
Good random number generators are (not so) easy to find
Selected papers from the 2nd IMACS symposium on Mathematical modelling---2nd MATHMOD
The influence of caches on the performance of sorting
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
ACM Transactions on Mathematical Software (TOMS) - Special issue in honor of John Rice's 65th birthday
Seeds for random number generators
Communications of the ACM - Wireless networking security
Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
Journal of Computational Physics
ANSS '07 Proceedings of the 40th Annual Simulation Symposium
Common defects in initialization of pseudorandom number generators
ACM Transactions on Modeling and Computer Simulation (TOMACS)
Communications of the ACM
An Algorithm Selection Approach for Simulation Systems
Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation
The event queue problem and PDevs
SpringSim '07 Proceedings of the 2007 spring simulation multiconference - Volume 2
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Handbook of Parametric and Nonparametric Statistical Procedures
Handbook of Parametric and Nonparametric Statistical Procedures
Algorithm portfolio design: theory vs. practice
UAI'97 Proceedings of the Thirteenth conference on Uncertainty in artificial intelligence
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Exploring the performance of spatial stochastic simulation algorithms
Journal of Computational Physics
Automating the runtime performance evaluation of simulation algorithms
Winter Simulation Conference
Selecting Simulation Algorithm Portfolios by Genetic Algorithms
PADS '10 Proceedings of the 2010 IEEE Workshop on Principles of Advanced and Distributed Simulation
An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Seven pitfalls in modeling and simulation research
Proceedings of the Winter Simulation Conference
Proceedings of the Winter Simulation Conference
Using workflows in M&S software
Proceedings of the Winter Simulation Conference
A generic adaptive simulation algorithm for component-based simulation systems
Proceedings of the 2013 ACM SIGSIM conference on Principles of advanced discrete simulation
Evaluating simulation software components with player rating systems
Proceedings of the 6th International ICST Conference on Simulation Tools and Techniques
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Stochastic simulation algorithms (SSA) are popular methods for the simulation of chemical reaction networks, so that various enhancements have been introduced and evaluated over the years. However, neither theoretical analysis nor empirical comparisons of single implementations suffice to capture the general performance of a method. This makes choosing an appropriate algorithm very hard for anyone who is not an expert in the field, especially if the system provides many alternative implementations. We argue that this problem can only be solved by thoroughly exploring the design spaces of such algorithms. This paper presents the results of an empirical study, which subsumes several thousand simulation runs. It aims at exploring the performance of different SSA implementations and comparing them to an approximation via 驴-Leaping, while using different event queues and random number generators.