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Figure 4 | BMC Bioinformatics

Figure 4

From: RuleMonkey: software for stochastic simulation of rule-based models

Figure 4

RuleMonkey is efficient for simulation of networks with fast reactions. The model considered here is specified in Additional file 4 (stiff.bngl). RuleMonkey (triangles) is compared with DYNSTOC (open dots). The y-axis indicates the total CPU time per reaction event required to simulate the kinetics of two first-order reactions. The x-axis indicates the value of ϕ, the ratio between the rate constants that characterize the two reactions. In RuleMonkey, the time step is sampled from an exponential distribution scaled by the total reaction rate (Eq. 5). In contrast, in DYNSTOC, the time step is fixed and limited by the rate of the fastest reaction [14]. This difference in how the time step is selected accounts for the performance differences seen for cases where ϕ ≫ 1.

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