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Secure access to patient data and analysis tools to run on that data will revolutionize the treatment of a wide range of diseases, by using advanced simulation techniques to underpin the clinical decision making process. To achieve these goals, suitable e-Science infrastructures are required to allow clinicians and researchers to trivially access data and launch simulations. In this paper we describe the open source Individualized MEdiciNe Simulation Environment (IMENSE), which provides a platform to securely manage clinical data, and to perform wide ranging analysis on that data, ultimately with the intention of enhancing clinical decision making with direct impact on patient health care. We motivate the design decisions taken in the development of the IMENSE system by considering the needs of researchers in the ContraCancrum project, which provides a paradigmatic case in which clinicians and researchers …