The goal of the Biological Input/Output Systems (BIOS) program was to develop a toolbox for the rational design and engineering of genetic regulatory circuits, signal transduction pathways, and metabolism. The utility of the toolbox components was demonstrated via the engineering of specific model laboratory organisms. Categories demonstrated include (1) the redesign of signal transduction pathways in plants and bacteria so they can be used together to make new functional signal transduction circuits; (2) the creation of logic circuits constructed out of components responsible for DNA rearrangements; and (3) the regulation of metabolic pathways via genetic regulatory and signal transduction components.