Many of today’s partially or fully automated medical research systems are rule, or constraint-driven systems that must be analyzed with respect to their rule compliance. We propose a new method called Multi Modeling Constraint-Driven System Analysis to explore and analyze rule conformance in these systems. Specifically, our method takes advantage of existing system documentation in the form of operational flow charts, and refines and transforms the information in them to into more formal system representations that allow automated analysis and reasoning, including reasoning about rule conformance. The method uses UML, Alloy, and protocol state machine models, and includes trace linking between informal and formal diagram and model elements, to allow analysis reporting on more informal diagrams and also ‘what if’ exploration to address atypical settings or problems found during analysis. Sometimes models are large and not amenable to automated analysis so we demonstrate how slicin...