I recommend this Matlab code for implementation of Monte Carlo method for sensitivity analysis of Simulink models: http://www.mathworks.com/matlabcentral/fileexchange/47758-sensitivity-analysis-in-simulink-models-with-monte-carlo-method
More resources, including demos and videos, for implementing and speeding up Monte Carlo simulations in both MATLAB and Simulink man be found here:
03 Jan 2012
Stochatic SIS Model
The model describes the classical stochastic SIS (Susceptible infected) Model.