Over the past decade, multi-level complex behavior and reactive nature of biological systems, has been a focus point for the biomedical community. We have developed a computational approach, termed Reactive Animation (RA) for simulating such complex biological systems. RA is an approach for describing the dynamic characteristics of biological systems based on facts collected from experiments. These data are integrated bottom-up by computational tools and methods for reactive systems development and are simulated concomitantly to a front-end user friendly visualization and reporting systems. Using RA, the experimenter may intervene mid-simulation, suggest new hypotheses for cellular and molecular interactions, apply them to the simulation and observe their resulting outcomes "on-line". Several RA models have been developed including models of T cell activation, thymocyte development and pancreatic organogenesis, which are describe in the in this review.