Fig. 4

The probabilistic method scales efficiently, and can be used to simulate the entire yeast MAP kinase network. The complete MAP kinase network [11] was used to generate models with variable k-base values. The top panels show the state evolution of all model species in the MAP kinase network model as a heat map. The average probabilities of active or inactive are calculated over 1000 time series of 125 time points. As the average probability increases, the color changes from blue (false) to yellow (true) gradually. p and k indicate false-rate and k-base, respectively. The initial setting was (turgor, MFalpha, Ste3, Tec1) = (true, false, false, true), but turgor was turned off at time t = 27, then switched on again at time t = 50 [13]. MFalpha was added at time t = 75. The individual state transitions of Hog1_[(T174)]-{P} and Slt2_[(Y192)]-{P} are shown in the middle and bottom panels. The rightmost panel shows a negative control in which all “K+” and “K-”contingencies were deleted