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Complex design, targeting system-on-chip based on reconfigurable 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.