The combination of mathematical modeling and novel experimental methods that probe the real–time dynamics of biological processes in vivo is emerging as a powerful approach to connect molecular mechanism to behavior in biology. It is now possible to build computational models that relate molecular events inside single cells to the behavior of these cells as they interact with the environment and with each other. Biologists can use dynamical modeling as a new tool to explore the dynamical consequences of a hypothesis before doing an experiment. Models help focusing biological questions and targeting experiments, which in turn impose constraints on the models. Close interaction between experimental studies and modeling is critical to success in this area and leads to the understanding of biological phenomena at the systems level.