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The analysis of transition in fully three-dimensional boundary layers on high-speed aircraft is hampered by the lack of a rigorous theory of instability in these flows and the lack of accurate data to evaluate approximations. To provide such data, we have in this first phase of a longer-term effort designed a computational framework for this task. This framework allows interactive computations and data analysis in connected blocks of the large physical domain on networks of computers. Theoretical studies on the stability of three-dimensional boundary layers have been performed to obtain guidance on the computational treatment of the problem. A multi-grid method specially adapted to the analysis of wave propagation in shallow domains has been developed and implemented. Testing of the code could not be completed before the project was terminated.