In Part I we learned how to set up simulation models and apply them to simple situations. We now turn our attention to the development of models of prototypic biological processes. To do so, we must specify numerical values for kinetic and other parameters. We thus begin by estimating reasonable numerical values of key quantities through order-of-magnitude procedures. We then examine the dynamic consequences of the stoichiometric structure of a network. Finally, regulatory mechanisms are examined to see how they change the natural mass action kinetic trends found in a network.