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This paper discusses the issues related to the correctness of agile manufacturing systems with distributed architectures. The corresponding development of software engineering methods targets the goal of easy-reconfigurable, self-organized software similar to that of the hardware. However, existing methods of software validation (manual testing or computer-aided simulation) are too slow to keep up with the pace of reconfigurations. In this paper we present an approach and a software tools to incorporate the formal verification to the practice of control engineering. The software package "verification environment for distributed applications" (VEDA) has been developed for model-based simulation and verification with a homogeneous graphical user interface. Net condition event systems are used for the modeling. VEDA deals with distributed controllers as defined in IEC 61499 and automatically generates the formal model of the controller with the given source code.