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Table 2 Run time and complexity comparisons of the ModelExplorer consistency checking algorithm “ExtraFastCC” against its predecessor “FastCC”

From: ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

    FastCC ExtraFastCC
Model # reacts # rev dead reacts # LPs time / s # LPs time / s
iTO977 1536 120 215 8.0 6 0.8
iJO1366 2583 241 489 27.2 6 9.0
Recon1 3719 395 794 117.6 21 7.9
  1. Disconnected reaction/metabolite clusters were discarded from every model before the testing in order to avoid unrealistically large LP numbers caused by running LPs on many small clusters. The first column shows the model name, the second shows the number of reactions in the model, and the third shows the number of blocked reversible reactions in the model. The numbers of reactions are recorded after disconnected-cluster purging. Note that the number of LPs used by FastCC is approximately equal to twice the number of dead reversible reactions. ExtraFastCC uses the open source solver Clp, while FastCC is run in Matlab using the much faster Gurobi [27] solver