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Microfluidics-based biochips are revolutionizing high-throughput sequencing, parallel immunoassays, clinical diagnostics, and drug discovery. These devices enable the precise control of nanoliter volumes of biochemical samples and reagents. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost due to smaller sample and reagent volumes, system integration, and less likelihood of human error. This keynote paper provides an overview of droplet-based “digital” microfluidics and outlines emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips from bioassay protocols.