I did however find some really solid examples for applying the work into MATLAB, but I have to figure it all out on how to apply it to my work. It's in this book, chapter 4 http://www.amazon.com/Gaussian-Markov-Random-Fields-Applications/dp/1584884320
. I have enough information to hit the ground running with respect to figuring it out now, so I'm no longer "lost". Pretty much after this step, instead of using SimuLink, I'm going to integrate all of the differential equations in MATLAB using the ode15s function http://www.mathworks.com/help/matlab/ref/ode15s.html?refresh=true
. I have done multiple programming projects, personal and school, that involved diffeq solvers in MATLAB so I should be good. Then I am going to apply the Metropolis-Hastings Sampling for the Markov chain Monte Carlo (but I am unsure if I can use the embedded MATLAB "solver" http://www.mathworks.com/help/stats/mhsample.html
or if I have to program all of it on my own, as some of the equations--3 out of 25 or so-- have "processes" that have intermediate steps--perhaps a for loop or a while loop would suffice for that "issue" and I could "pass the current value" for those current equations that way...)...then I will be done with the first part of my project. So the end is definitely in sight.