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We present an end-to-end tool-chain for model-based design and analysis of component-based embedded real-time software, with avionics mission computing as an application domain. The tool-chain covers the entire system development lifecycle including modeling, analysis, code generation, and run-time instrumentation. Emphasis is placed on integration of tools developed by multiple institutions via standardized interface format definitions in XML. By capturing all relevant information explicitly in models at the design level, and performing analysis that provides insight into non-functional aspects of the system, we can raise the level of abstraction for the designer, and facilitate rapid system prototyping.