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Auto-Pipe is a tool that aids in the design, evaluation and implementation of applications that can be executed on computational pipelines (and other topologies) using a set of heterogeneous devices including multiple processors and FPGAs. It has been developed to meet the needs arising in the domains of communications, computation on large datasets, and real time streaming data applications. This paper introduces the Auto-Pipe design flow and the X design language, and presents sample applications. The applications include the Triple-DES encryption standard, a subset of the signal-processing pipeline for VERITAS, a high-energy gamma-ray astrophysics experiment. These applications are discussed and their description in X is presented. From X, simulations of alternative system designs and stage-to-device assignments are obtained and analyzed. The complete system will permit production of executable code and bit maps that may be downloaded onto real devices. Future work required to complete the Auto-Pipe design tool is discussed.