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When reconfigurable devices are used in modern embedded systems and their capability to adapt to changing application requirements becomes an issue, comprehensive modeling and design methods are required. Such methods must respect the whole range of functionality of the reconfigurable fabrics. In particular, the heterogeneity and reconfiguration delay of modern FPGAs are important details. Comprehensive methods to exploit these characteristics within the integrated design of embedded systems are still not available. In this paper, we introduce a synthesis methodology for reconfigurable systems that respects the specific requirements of run-time reconfiguration. The methodology bases on profound concepts, and expands known notations and model techniques.