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The emerging need for large amounts of flexible computational power on embedded devices motivated many researchers to incorporate reconfigurable logic together with an instruction-set-processor (ISP) into their architectures. This implies that tomorrow's applications will make use of both the ISP and the reconfigurable logic in order to provide the user with maximum performance. Today, however, a few stumbling blocks prevent these kinds of heterogeneous architectures from becoming mainstream. The technology still lacks a form of run-time management infrastructure. This infrastructure should ease application development by shielding the programmer from the complexity of the system and by providing a clear application development API. This paper presents a novel approach for designing an operating system for reconfigurable systems (OS4RS). Creating such an operating system is an integral part of our ongoing research regarding reconfigurable computing. An initial version of our operating system was used to manage a reconfigurable systems demonstrator.