Note this one though, from the Petri net web page:

* Darren J. Wilkinson, _Stochastic Modelling for Systems Biology_, Taylor & Francis, New York, 2006. Good introduction to stochastic Petri nets, with applications to gene expression and the [[Lotka-Volterra equations]] for predator-prey interactions.

This has a short chapter called case studies, with the following applications and simulation challenges:

* Dimerisation kinetics
* Michaelis-Menten enzyme kinetics
* An auto-regulatory genetic network
* The lac operon

I was hoping for a more basic text to start with, and one that covered a wider range of applications, but for the time being we can use it as a working text. We can discuss some of the simulation challenges on a new thread, and who ever is up for it can try their hand at coding them up and sharing their results.

These are small, homework level simulations, which can be done on any laptop in anyone's language of choice.

@DanielGeisler if you are interested in digging into this subject, I recommend getting this textbook. Although oriented to biology, it gives a broader theoretical foundation.