The article describes a new model of agent modeling as a tool of researching complicated heterogenic decentralized socio-economic systems. It was shown that agent modeling provides an opportunity to solve problems of high complexity, in particular researching complex heterogenic decentralized socio-economic systems with regard to psycho-social and psycho-emotional aspects of actors’ behavior, like those systems studied in examples of the present research. A new methodology of using models for imitation modeling of dynamic social-economic processes was designed. On the basis of methodology proposed by the authors an innovation, effective informational system to research organizational structures with regard to psycho-social aspects for typical actors, their customers and typical actions was developed. The article provides examples of the impact of organization structures on their functioning and viability. It was shown that open applied tools can be used to analyze the efficiency of organizational social-economic systems, their viability and functioning providing competitiveness of the system. An example of using the designed tools in connection with the research of efficiency of reorganizing the elements of the structure ’University’ as a model of the higher education institution. The authors put forward a number of recommendations aimed at organization of elements of the system ‘University’.
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