How good is our understanding of the way cells treat information and make decisions? To what extend our current understanding enables us to reprogram and control the way cells behave? In this manuscript I describe several approaches developed for the computational analysis of the dynamics of biological networks. In particular I present work done on (i) the analysis of large gene networks with partial information on parameter values, (ii) the use of specification languages to express observations or desired properties in an abstract manner and efficiently search for parameters satisfying these properties, and (iii) recent efforts to use models to drive gene expression in real-time at the cellular level.
