The paper describes several models, Mi, i=1...n, where M0 correspond to the unperturbed model and all the others correspond to the perturbed model. This model is the unperturbed model. The model reproduces figure 5 of the reference publication. The figures were generated by running 1 simulation, whereas in the paper the plotted values are the means of 800 simulations using randomly samples parameter sets.  

Additional information from the Author:

The parameter that were randomly samples are the transcription parameters c_Proteins... and k_Proteins. The parameter were sampled from a lognormal distribution with sigma = 1.5 and mu = 0.5