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This paper accompanies a tutorial session at the 2015 American Control Conference, and provides a survey of emerging technologies and research problems at the boundary between systems engineering, neuroscience and neural medicine. Emphasis will be placed on both recent theoretical developments - for example, system identification and controllability in neuronal networks - and real-world constraints in applications such as clinical deep brain stimulation, or optical stimulation in experimental neuroscience. Discussion will extend to how these constrains may necessitate the development of entirely new paradigms in systems and control theory that respond to the unprecedented challenges facing neural scientists and engineers.