HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

Table 2

Simulation running times of HSimulator and of the state-of-the-art simulator COPASI. Except for the deterministic simulation, HSimulator is demonstrated to be faster in all the considered scenarios (FCM indicates the fully connected model; MSM indicates the multiscaled model). The considered models were simulated for time units (MAPK and fully connected model), 12 time units (Gemcitabine), and 10 time units (multiscaled model).

Algorithm	MAPK	Gemcitabine	FCM	FCM	MSM	MSM
COPASI - DM	2.39 sec.	0.88 sec.	5.09 sec.	415.04 sec.	28.87 sec.	262.1 sec.
HSimulator - DM	2.23 sec. (−6%)	0.7 sec. (−12%)	1.61 sec. (−68%)	168.75 sec. (−59%)	11.0 sec. (−62%)	120.84 sec. (−54%)
HSimulator - RSSA	2.03 sec. (−15%)	0.66 sec. (−25%)	1.10 sec. (−78%)	77.46 sec. (−81%)	4.25 sec. (−85%)	37.23 sec. (−86%)
COPASI - LSODA	0.06 sec.	0.02 sec.	0.56 sec.	0.08 sec.	0.08 sec.	0.21 sec.
HSimulator - RK45	0.06 sec. (+0%)	0.04 sec. (+100%)	0.001 sec. (−99%)	0.001 sec. (−99%)	0.13 sec. (+63%)	0.52 sec. (+148%)
COPASI - Hyb. RK	0.21 sec	0.54 sec.	26.74 sec.	14.67 sec.	1.93 sec.	35.49 sec.
HSimulator - HRSSA	0.1 sec. (−52%)	0.38 sec. (−30%)	1.10 sec. (−96%)	0.8 sec. (−95%)	2.53 sec. (−31%)	5.89 sec. (−83%)