Traditionally molecular biology research has tended to reduce biological pathways to composite units studied as isolated parts of the cellular system. With the advent of high throughput methodologies that can capture thousands of data points, and powerful computational approaches, the reality of studying cellular processes at a systems level is upon us. As these approaches yield massive datasets, systems level analyses have drawn upon other fields such as engineering and mathematics, adapting computational and statistical approaches to decipher relationships between molecules. Guided by high quality datasets and analyses, one can begin the process of predictive modeling. The findings from such approaches are often surprising and beyond normal intuition. We discuss four classes of dynamical systems used to model genetic regulatory networks. The discussion is divided into continuous and discrete models, as well as deterministic and stochastic model classes. For each combination of these categories, a model is presented and discussed in the context of the yeast cell cycle, illustrating how different types of questions can be addressed by different model classes.