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This paper addresses solutions on integration and reuse of heterogeneous distributed controllers. In particular it shows the way to integrate the emerging IEC 61499 standard into the established IEC 61131 automation frameworks. It is illustrated on example of a modular manufacturing cell with distributed control units, how to realize distribution of heterogeneous controllers using the IEC 61499 standard and how to integrate these controllers into the plant formerly controlled by distributed PLCs. Therefore, methodologies and patterns for the design of distributed controllers and their implementation variants are introduced. In addition, the paper describes the details of a higher level communication protocol used to implement interaction between the modules. A framework for the simulation of IEC 61499 applications is also introduced.