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. Author manuscript; available in PMC: 2023 Aug 31.
Published in final edited form as: Lett Biomath. 2023 May 26;10(1):87–103.

Table 2:

Total simulation time (in seconds) comparison for GillesPy2 Solvers and StochKit2 (Sanft et al., 2011) for popular biochemical models. Times reported are the total time (compile + simulation) for a single trajectory. See Figure 6 for an example of performance versus ensemble size.

Model SSA SSA C++ Tau-Hybrid Tau-Hybrid C++ Tau-Leaping Tau-Leaping C++ StochKit2 (SSA)
Decay 0.00312 3.893 0.0610 16.292 0.00605 8.015 0.0406
Dimerization 0.00338 3.829 0.125 13.464 0.0132 7.493 0.0764
Michaelis-Menten 0.0654 4.573 0.797 17.010 0.0711 7.861 0.0743
Genetic Toggle Switch 0.0876 3.085 1.457 16.22 0.0885 6.800 7.623
Tyson 2-state Oscillator 21.16 3.164 303.1 14.29 22.16 6.807 6.984
Vilar Oscillator 15.29 3.167 299.5 14.42 31.72 8.301 0.223
Multi-Event model N/A N/A 0.246 16.22 N/A N/A N/A
SBML features model N/A N/A 0.586 N/A N/A N/A N/A