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An automated warehouse system has two main components: an automated storage and retrieval subsystem consisting of a number of aisles, each one served by a crane, and a picking area which is formed by bays where stock units coming from the aisles are partially emptied by human operators. These two components are connected via an interface area consisting of carousels, conveyors, and buffers. This area is usually modeled as a discrete event system, while the overall system performance depends also on continuous time phenomena. Part I presents a hybrid model based on a new Petri net formalism that merges the concepts of Hybrid Petri Nets and Colored Petri Nets to obtain modular and compact models for these systems. An example is discussed in detail to motivate the introduction of a new formalism. A control oriented simulation tool is also presented. Part II will focus on the application of this formalism to automated warehouse systems analysis and performance evaluation. Finally, a real case study is considered to show the effectiveness of the approach.