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The automated control of mechanical ventilation requires the merging of the disciplines of control engineering and clinical knowledge from intensive care medicine. To design and accurately implement the clinical expertise it is of paramount importance to keep clinicians involved throughout the programming phases to accommodate dynamic changes in mechanical ventilation strategies. A rapid control prototyping system is presented which allows the quick implementation and testing of new control laws. Furthermore, by choosing a graphical programming language, the clinicians remain on-board. An automated compliance-based PEEP titration and rule-based FiO2 control are shown as exemplary results for oxygenation control during protective ventilation using MATLAB Stateflow®