Enumeration of smallest MCSs (synthetic reaction lethals) disabling growth in a genome-scale network model of E.coli.

MCSs (synthetic reaction lethals) that disable growth in an E. coli genome-scale metabolic network with glucose as sole carbon source. The full/compressed networks contain 1668/562 metabolites and 2382/936 reactions. For computation 12 threads on a cluster node with two Intel Xeon DP X5650 processors (each 6 cores) were used. The computation time given in each row specifies the time needed to calculate the MCSs of the respective size. The total computation time for MCSs of size 1–5 was thus ∼430 h. In order to get comparable run times the SL Finder was executed on the same computer with GAMS 24.1.3 (using CPLEX 12.5.1 as solver). All physical memory was made available and up to 9 GB were used during optimization. The MCSEnumerator calculations were also done on a typical desktop PC with a quad-core CPU (Intel(R) Core(TM) i5-3570, 3.40 GHz) showing that the computation times increase only moderately by approximately 50%.*)Only 226 synthetic triple lethals (which are all contained in the MCSs found by MCSEnumerator) could be calculated after which optimization could not be continued due to numerical problems reported by the solver.