ABSTRACT
This chapter starts the discussion on design-automation challenges associated with biomolecular assays. It first describes a benchtop experimental study, which was carried out to understand gene-expression analysis and its relationship to the biochip design specification. Motivated by this experimental work, an integrated framework for quantitative gene-expression analysis using digital microfluidics is illustrated. The proposed framework includes: (i) a spatial-reconfiguration technique that incorporates resource-sharing specifications into the synthesis flow; (ii) an interactive firmware that collects and analyzes sensor data based on quantitative polymerase chain reaction; (iii) a real-time resource-allocation scheme that responds promptly to decisions about the protocol flow received from the firmware layer. This framework is combined with cyber-physical integration to develop the first design-automation framework for quantitative gene expression. Simulation results show that this framework efficiently utilizes on-chip resources to reduce time-to-result without sacrificing the chip's lifetime.
