Figure 3.

Running time for simulations of genome-wide genetic perturbations. Running time of genome-wide in silico perturbation experiments (single- and double-gene knockouts) using various software packages and different mathematical optimisation packages. a) For computation of single flux deletions, we used the functions oneFluxDel() in sybil, single_deletion() in COBRApy, singleRxnDeletion() in the COBRA Toolbox, and Exhaustive_single_deletion() in abcdeFBA. b-d) In sybil, we used the functions oneGeneDel() and doubleGeneDel() for simulations of single and pairwise knockout mutants, respectively. The same results were achieved with the COBRA Toolbox using functions singleGeneDeletion() and doubleGeneDeletion(), respectively. In COBRApy, we used functions single_deletion() and double_deletion. In OptFlux, the calculation of so called "critical genes" was used. The running times for COBRApy are extremely long when using the IBM ILOG CPLEX solver (* more than 24 hours for a simulation of all pairwise knockout mutants). The interface between COBRApy and IBM ILOG CPLEX seems not to support reusing a computed basis for re-solving an optimisation problem. Running times were obtained as in Figure 2.