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By allowing human users to manipulate simulation models and steer their execution at run time, interactive simulation systems (ISS) are essential to realise problem solving environments (PSE) for studying complex problems that are difficult to investigate using conventional methodologies. However, the complexity of system development critically hampers the construction of ISSs; when a scientist explores a complex problem, he has to spend much of his effort on various implementation issues, instead of on the investigation of the experiment itself A layered framework for developing ISSs is crucial to hide the underlying development issues from scientists and to allow them to focus on the high-level behaviour of the system. In this paper we investigate a solution to the complexity issues in ISSs based on the separation of application logic control and system functionality. We implement a proof of concept architecture, called interactive simulation system conductor, based on high level architecture (HLA), and demonstrate that this architecture allows a scientist to quickly adapt the system to his needs in a rapid prototyping approach. A medical application for planning surgical operations is used as a test case.