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Uncovering the dynamic behavior of biochemical networks is one of the systems' biology's tasks. These systems are very complicated systems, containing many interacting components. Recently, researchers have tested computational tools to model these systems in order to elucidate the organizational principles. In this paper we recommend using Holonic Multiagent systems for biological networks simulation. Holonical systems guarantee to provide a recursive and hierarchical modeling for complex systems with dynamic and runtime reorganization. They are adopted for simulation where systems have a hierarchical structure and can be decomposed into individual cooperating entities.