Hi Frank,
Unfortunately, SimBiology does not currently provide direct access to the calculated rates. There are a couple of options for working around this limitation. If you are interested in the total rate of change of a species, then the easiest way to estimate that is probably by finite-differencing the simulation results. For example:
m1 = sbiomodel('example');
c = m1.addcompartment('c');
s = m1.addspecies('s', 100);
k = m1.addparameter('k', 0.5);
r = m1.addreaction('s -> null', 'ReactionRate', 'k*s');
[t1,y1] = sbiosimulate(m1);
dy_dt = diff(y1) ./ diff(t);
Or if you have a few reactions that you want to know the rate of, you can calculate them directly from the rate expression. You can either add this result directly to the simulation results by creating a repeated assignment rule or by calculating it after the simulation. For example, continuing from the example above:
rate1 = k.Value*y1;
m1.addparameter('rate', 'ConstantValue', false);
m1.addrule('rate = k*s', 'repeatedAssignment');
[t2, y2] = sbiosimulate(m1);
rate2 = y2(:,2);
plot(t1(1:end-1),-dy_dt, 'x-', t1, rate1, 'o-', t2, rate2, '+-')
Hopefully that is a sufficient workaround. Good luck!
-Arthur