Despite their central importance, the basic architecture and temporal dependencies underlying most eukaryotic gene programs are poorly understood. Such an understanding is essential if we wish to explain how cells integrate multiple stimuli using a limited vocabulary of signaling molecules, to create a vast multiplicity of behaviors. Using time-explicit models of regulatory cascades, we can start to define regulatory events underlying specific decision-points in cells undergoing short-term differentiation. In the lab we use such tools to study dendritic cell (DC) differentiation in the antiviral response. Identifying for the first time the precise timing leading to a functioning anti-viral response. Another avenue in which we are brining more dynamical models to the study of intracellular signaling in immune cells is in the study of Ca2+ flux. Ca2+ flux and action potentials have been known for some time to be a major signaling factor in neurons. Where they are tightly linked to learning and neuronal development. Only recently have imaging methods matured allowing us to study how the fluctuations and control of Ca2+ relate to the internal signaling of activated immune cells. We are developing methods to analyze this data and create models of the temporal control of Ca2+ in immunity.