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The book gives an overview of the most important solutions to a series of problems that usually occur in manufacturing systems, focusing on those solutions that are based on a formal model of the system. The main problems considered are modeling and simulation, supervisory control (including deadlock prevention), performance evaluation (including scheduling and optimization), fault diagnosis, and reconfiguration. The book also presents formal methods in detail for specific problems in the above framework. All are illustrated with examples from manufacturing. The book assumes some knowledge of systems theory and discrete event systems theory but provides introductory material on each formalism (Petri nets, automata, and max-plus algebra), making the book suitable also for readers who are not experts on formalisms.