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In computer-based control systems, embedded software is taking over what mechanical and dedicated electronic systems used to do, that is, to engage and control the physical world, interacting directly with sensors and actuators. Therefore, software running on a digital processor is tightly-coupled with its surrounding physical environment. We propose an integrated approach based on Timed Petri-Nets for modeling and analysis of embedded real-time systems where real-time scheduling behavior of the controller software is explicitly represented at the model-level, together with the physical environment that it interacts with. This enables the designer to have an integrated view of the entire system while analyzing the system and making design decisions. We also describe a syntax-directed, automated translation procedure from Timed Petri-Nets to Timed Automata, thus enabling the use of model checkers such as UPPAAL for analysis purposes. We consider the railroad crossing problem as an application example, and evaluate alternatives for controller implementation on either single-processor or distributed multi-processor platforms based on the integrated approach.