Table 2.
Comparison of FVA and ll-FVA, performed on models spanning a wide range of sizes
| Model | Number of reactions | FVA time (s) | ll-FVA time (s) | Time per iteration (s) | Number of changed reactions | % of model changed | Number of deactivated reactions | Changed reactions |
|---|---|---|---|---|---|---|---|---|
| Toy network | 5 | 0.08 | 0.19 | 0.04 | 3 | 60.00% | 0 | v1 v2 v3 |
| Core E. coli | 95 | 1.1 | 7.35∗ | 0.08 | 2 | 2.11% | 0 | FRD7 SUCDi |
| H. pylori iIT341 | 554 | 7.8 | 123 | 0.22 | 22 | 3.97% | 6 | 4HGLSD ACKr AHSERL2 H2CO3D H2CO3D2 HCO3E HPROa HPROx HSERTA HSK METB1r NAt3_1 PHCD PHCHGS PROt2r PROt4r PTAr SHSL1r SHSL2r SHSL4r THRD_L THRS |
| S. aureus iSB619 | 730 | 12.1 | 604 | 0.83 | 6 | 0.82% | 1 | FLDO FMNRx GLUt2 GLUt2r NADTRHD NAt3 |
| E. coli iAF1260 | 2382 | 58.8 | 18222∗∗ | 7.6 | 68 | 2.85% | 7 | ABUTt2pp ACACT1r ACCOAL ACKr ACS ACt2rpp ACt4pp ADK1 ADK3 ADNt2pp ADNt2rpp ALATA_L CA2t3pp CAt6pp CRNDt2rpp CRNt2rpp CRNt8pp CYTDt2pp CYTDt2rpp GLBRAN2 GLCP GLCP2 GLCS1 GLCtex GLCtexi GLDBRAN2 GLGC GLUABUTt7pp GLUt2rpp GLUt4pp GLYCLTt2rpp GLYCLTt4pp HPYRI HPYRRx ICHORS ICHORSi INDOLEt2pp INDOLEt2rpp INSt2pp INSt2rpp KAT1 NAt3pp NDPK1 PPAKr PPCSCT PPKr PPM PROt2rpp PROt4pp PRPPS PTA2 PTAr R15BPK R1PK SERt2rpp SERt4pp SUCOAS THMDt2pp THMDt2rpp THRt2rpp THRt4pp TRSARr URAt2pp URAt2rpp URIt2pp URIt2rpp VALTA VPAMT |
| Human Recon 1 | 3742 | 199.95 | 111163 | 29.7 | 34 | 0.91% | 10 | 10FTHFtm 25HVITD2t 25HVITD2tm 4HGLSDm ACCOAtn ACHtn CHAT CHATn CHOLtn COAtn CYTK1n CYTK2n DCK1n DCK2n GALT H2CO3D2m H2CO3Dm HCO3Em NADHtpu NADtpu NDPK1n NDPK2n NDPK3n NDPK5n NDPK7n NDPK8n NNATr P5CRx PHCDm PHCHGSm PPDOx UMPKn VITD3t VITD3tm |
∗
Standard deviation of 0.3 s across four different growth conditions and two different objective functions.
∗∗
Standard deviation of 6358 s across four different growth conditions and two different objective functions.