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Microchip structures represent an attractive platform for microscale chemical processing of fluidic systems. However, standardized design methods for these devices have not yet been developed. Here we describe our work toward adapting traditional SoC circuit design techniques for the synthesis of fully customized and multiplexed lab-on-a-chip (LoC) devices. We discuss our formulation of the multiplex layout problem and present an approach for the design of microchip based electrophoretic separation systems. This work is extendable to systems incorporating mixing and reaction.