Controlling the differential expression of many thousands of genes is the most fundamental task of a developing organism. It requires an enormous computational device that has the capacity to process in parallel a vast number of regulatory inputs in the various cells of the embryo and come out with regulatory outputs that are tissue specific. The regulatory genome constitutes this computational device, comprising many thousands of processing units in the form of cis-regulatory modules. The interconnected cis-regulatory modules that control regulatory gene expression create a network that is the underlying mechanism of specification. In this review we use the gene regulatory network that governs endomesoderm specification in the sea urchin embryo to demonstrate the salient features of developmental gene regulatory networks and illustrate the information processing that is done by the regulatory sequences.