The creation of miniature biochemical analysis systems using microfavrication technology is a recent significant development in the field of micofluidics. These systems offer advantages such as size reduction, power reduction, and increased reliability. However, current systems are tailored to a specific task, and thus are unable to be reconfigured and reprogramed to handly a variety of tasks. This invention is a method for the layout, design and control of Digital Microfluidics Systems (DMFS) using discrete droplets on a planar array of electrodes.DMFS can be used for biochemical analyses, such as DNA Polymerase Chain Reaction. The layout design and routing algorithms of this new method allow the same physical array to be used for a variety of biochemical analyses, even allowing the concurrent execution of multiple analyses.