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A model structure is proposed for the design and evaluation of greenhouse factories equipped with an automated system for transportation of half products. The model is set up according the process interaction method. The system control decisions are made decentralized by a number of system elements and are modeled and clearly identifiable at several levels in the model. A series of experiments with a prototype model is carried out and presented. The possibilities of re-using the control part of the model in a real system as well as the potential of the design tool are discussed.