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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization

Fig. 4

Comparing the runtimes of PSOMCS and GAMCS. a Plotting the runtimes of PSOMCS and the GA we had previously implemented clearly shows PSOMCS is orders of magnitude faster than GAMCS. Note that the time axis is logarithmic and that both algorithms reach the same maximum fitness. The change in knockout sizes are indecated by the numbers along the line. b Both methods also produce similar designs, an example of which is shown. This design is obtained with 5 knockouts (R_GND R_SUCOAS R_MALS R_ACt2r R_LDH_D). The plot was generated by applying the knockouts on the complete set of 429275 EFMs of the Escherichia coli core model. R_norm is the sum of uptake rates for the five carbon substrates, glucose, galactose, mannose, arabinose and xylose under aerobic conditions

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