Table 4.
Runtime and number of solved LPs for double reaction knockouts (Algorithm 2)
| Model | Step | Total | |||
|---|---|---|---|---|---|
| Blocked | Couples | dko | |||
| E. coli iJO1366 | LPs | 1718 | 9943 | 133225 | 144886 |
| time | 2.0 | 42.2 | 4016.4 | 1h 8min | |
| E. coli iAF1260 | LPs | 1679 | 10780 | 52112 | 64571 |
| time | 1.7 | 31.5 | 2688.2 | 45min 21s | |
| S. cerevisiae iND750 | LPs | 597 | 3987 | 90664 | 95248 |
| time | 0.33 | 6.8 | 397.8 | 6min 45s | |
| M. tuberculosis iNJ661 | LPs | 327 | 3416 | 20647 | 24390 |
| time | 0.33 | 5.6 | 177.7 | 3min 4s | |
| S. aureus iSB619 | LPs | 144 | 3638 | 19477 | 23259 |
| time | 0.09 | 2.8 | 43.2 | 46.0s | |
| H. pylori iIT341 | LPs | 106 | 1812 | 6753 | 8671 |
| time | 0.06 | 1.9 | 18.0 | 20.0s | |
| E. coli textbook | LPs | 26 | 341 | 1739 | 2106 |
| time | 0.004 | 0.06 | 0.62 | 0.68s | |
The computation was done in three steps: Calculation of the blocked reactions, flux coupling analysis to determine the coupled reactions, and finally the double knockout simulations.
Times are given in seconds if not specified otherwise (numbers may not add up due to rounding errors).