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Summary form only given. Microfluidics-based biochips (or lab-on-chip) are revolutionizing laboratory procedures in molecular biology, and leading to a convergence of information technology with biochemistry and nanoelectronics. Advances in microfluidics technology offer exciting possibilities for high-throughput DNA sequencing, protein crystallization, drug discovery, immunoassays, neo-natal and point-of-care clinical diagnostics, etc. As microfluidic lab-on-chip mature into multifunctional devices with “smart” reconfiguration and adaptation capabilities, automated design and ease of use become extremely important. Computer-aided design (CAD) tools are needed to allow designers and users to harness the new technology that is rapidly emerging for integrated biofluidics. This talk will present ongoing work at Duke University on design automation techniques for microfluidic biochips. First, the speaker will provide an overview of electrowetting-based digital microfluidic biochips. Next, the speaker will describe synthesis tools that can map bioassay protocols to a reconfigurable microfluidic device and generate control software, an optimized schedule of bioassay operations, the binding of assay operations to functional units, and the layout and droplet flow-paths for the biochip. Techniques for pin-constrained chip design, fault detection, and dynamic reconfiguration will also be presented. An automated design flow allows the biochip user to concentrate on the development of nano- and micro-scale bioassays, leaving implementation details to CAD tools.