Table 1. Run time and reactions per second for different simulators.

The fission yeast model is executed until 1000 minutes (20 replications). The values in parenthesis refer to executing ML-Rules 3 as WebAssembly code. The ML-Rules 2 implementation of the model contains ten species and 20 rules. The ML-Rules 3 version of the model consists of 7 species and 20 rules. The model starts with two cell compartments and ends with about 12. During the simulation time, the model undergoes about 10 structural changes and half a million static reactions.

simulator	runtime [s]	throughput [1000/s]
ML-Rules 2	12.4	40.8
ML-Rules 3	0.124 (0.190)	4190 (2690)
ML-Rules 3—network free	0.321 (0.352)	1590 (1440)
ML-Rules 3—w/o templates	0.259 (0.331)	1950 (1530)