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Today's advanced technology engines have a high content of electronic actuation requiring sophisticated real-time embedded software sensing and control. To enable research on such engines, a system with a flexible engine control unit (ECU) that can be rapidly configured and programmed is desired. Such a system is being used in the Advanced Internal Combustion Engine (AICE) Laboratories at Michigan Tech University (MTU) for research on a multi-cylinder spark-ignited gasoline, a high pressure common rail diesel and a single cylinder alternative fuels research engine. The system combines a production ECU with a software development system utilizing Mathworks Simulink/Stateflow © modeling tools. The interface in the Simulink modeling environment includes a library of modeling and interface blocks to the production Operating System (OS), Low Level Drivers (LLD) and CAN-based calibration tool.