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In this paper, we present a case study for the design, programming and usage of a reconfigurable system-on-chip, MorphoSys, which is targeted at computation-intensive applications. This 2-million transistor design combines a reconfigurable array of cells with a RISC processor core and a high bandwidth memory interface. The system architecture, software tools including a scheduler for reconfigurable systems, and performance analysis (with impressive speedups) for target applications are described.