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Table 1 Comparisons between StochKit, the SSA implementation on the R-System and our approach for a MM reaction scheme.

From: Modelling non-Markovian dynamics in biochemical reactions

  Gecode R-System StochKit
2 Time Iterations Time Iterations Time Iterations
100 0.28 500 1.10 10412.40 0.04 5
101 0.35 500 28.78 99929.2 0.11 48
102 0.39 500 1855.92 990849.5 0.26 500
103 0.43 500 - - 0.78 5000
104 0.42 500 - - 7.75 50000
105 0.39 500 - - 77.50 500000
  1. Times in seconds reported correspond to the average of 10 runs. Constants k1 and k3 were set to 10 and k2 varies as shown in the table. The initial concentrations of S and E were set to 100000 and 100 molecules, respectively.