A central goal of the Center for Synthetic Biology is to develop the high throughput experimentation tools that will allow the optimization and understanding of multi-component biosynthetic transformations. Even modest biosynthetic processes may require several enzymes, a number of cofactors, and defined ionic and metabolic components in the buffer — where the optimal environment for one enzyme may compromise activity of another. Hence, there are a staggering number of theoretical reaction designs that can be successful in producing the desired product, but the practical limitations now faced in assembling and testing each one severely limit those that can be tested. High throughput screening tools initially developed in drug discovery now provide a route toward technologies that are tailored for the rapid design, identification, and understanding of optimal biosynthetic pathways. Work in this theme combines the engineering platforms, parallel expression of proteins, and computational analysis to identify design rules in the data.