Figure 3
From: RuleMonkey: software for stochastic simulation of rule-based models
RuleMonkey is efficient for simulation of rule-based models characterized by large-scale networks. We compare RuleMonkey (solid lines marked by triangles), DYNSTOC (solid lines marked by open dots) and a problem-specific implementation of the method of Yang et al. [19] (dotted lines); these methods are used to simulate the TLBR model. a) Scaling of computational cost with system size, where size is measured by N R , the number of cell-surface receptors. b) Scaling of computational cost with dimensionless parameter β = N R k+2/koff, which controls the (equilibrium) extent of ligand-induced receptor crosslinking. The rate constant k+2 characterizes receptor crosslinking, and the rate constant koff characterizes dissociation of ligand-receptor bonds. The value of β was adjusted by varying k+2 while holding N R = 300 and koff = 0.01 s-1 fixed. In each panel, the y-axis indicates the normalized total CPU time per reaction event required to simulate the kinetics of the TLBR model from time t = 0 to 1000 s with all ligand initially free. Parameters used are the same as those reported for Fig. 3 of Colvin et al. [14]. See the BioNetGen input file testcase2a.bngl (Additional file 2).