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The complexity of today's experiments in High Energy Physics results in a large amount of readout channels which can count up to a million and above. The experiments in general consist of various subsystems which themselves comprise a large amount of detectors requiring sophisticated DAQ and readout electronics. We report here on the structured software layers to control such a data acquisition system for the case of LHCb which is one of the four experiments for LHC. Additional focus is given on the protocols in use as well as the required hardware. An abstraction layer was implemented to allow access on the different and distinct hardware types in a coherent and generic manner. The hierarchical structure which allows propagating commands down to the subsystems is explained. Via finite state machines an expert system with auto-recovery abilities can be modeled.