For more complex examples of stochastic Petri net, see:
* Monika Heiner, [From Petri nets to differential equations: an integrative approach for biochemical network analysis](https://www-dssz.informatik.tu-cottbus.de/publications/slides/2005_muenchen_msbf.sld.pdf), Brandenburg University of Technology Cottbus, Dept. of CS, May 2005.
There is one net for a chemical reaction:
\\[2 NAD^+ + 2 H_2 O \rightarrow 2 NADH + 2 H^+ + O_2\\]
Here the species are molecules, and the transitions are chemical reactions.
Note this is using the standard graphical notation for Petri nets, which is a directed bipartite graph, with circles for the species and squares for the transitions. There is a directed edge from a circle to a square whenever the corresponding species is input to the corresponding transition, and similarly an edge from a square to a circle whenever the transition outputs to the species.
Those slides also contain a more complex Petri net, for a biochemical reaction network (the "RKIP pathway").