method | IOS, LSODA | IOS, Rosenbrock | SSA, single (ens.) |
|---|
BCI | 18.2s (18.5s) | 59.5s (59.8s) | 0.04s (0.5h) |
JIT | 0.9s (3.6s) | 13.0s (35.8s) | 0.03s (0.4h) |
- Execution times of iNA's timecourse analysis for IOS and SSA for the gene oscillatory network reproducing Additional file 3 (a) and (b), respectively. The table compares the IOS method using the ODE integrator LSODA and Rosenbrock in combination with a bytecode interpreter or iNA's JIT feature. The value in the brackets denotes the overall time including bytecode assembly or JIT compilation. The SSA value denotes the average time for a single run while the values in the brackets denote the extrapolated value for an ensemble of 50, 000 independent realizations needed to generate Additional file 3 (b). Benchmarks were performed on Ubuntu (64bit), Dell OptiPlex 9010 SF, Core i7-3770 @ 3.4GHz using a single core.
