Figure 5

Runtime Comparisons. The EGF signaling pathway described by Lee et al. [38] was simulated with the three exact methods provided by FERN (original and enhanced Gillespie algorithm and the next reaction method by Gibson and Bruck) for a simulated time of 800 seconds both with an SBML network using expression trees to represent MathML expressions and a FernML network. For each combination of network type and stochastic simulation algorithm, 1,000 simulations were performed and the average runtime in milliseconds was calculated. The same simulations were performed with the Gillespie and Gibson-Bruck algorithms of ISBJava. All results were obtained on one processor of an Intel Core2Duo with 2.4 GHz. Standard errors in all cases were < 1.5 milliseconds.