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Complex design, targeting System-on-Chip based on recon-figurable architectures, still lacks a generalized methodology allowing both the automatic derivation of a complete system solution able to fit into the final device, and mixed hardware-software solutions, exploiting partial reconfiguration capabilities. The Shining methodology organizes the input specification of a complex System-on-Chip design into three different components: hardware, reconfigurable hardware and software, each handled by dedicated sub-flows. A communication model guarantees reliable and seamless interfacing of the various components. The developed system, stand-alone or OS-based, is architecture-independent. The Shining flow reduces the time for system development, easing the design of complex hardware/software reconfigurable applications.