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We introduce a novel methodology to formally specify complex multi-agent systems. Our approach allows us to redefine computational problems in terms of agents that perform certain tasks. In our view, a system is formed by the combination of atomic and complex agents. Atomic agents are in charge of executing atomic tasks while complex agents reunite and summarize the properties of their underlying atomic agents. Basically, our approach consists in specifying the smaller parts of the problem as atomic agents. Each atomic agent is in charge of executing a small transformation of resources. Afterwards, the system will recombine them to form complex agents that will embrace the knowledge of several atomic agents. All agents are located on a superstructure of communication cellules created to record the hierarchy of the tasks. In order to provide a useful framework, we have developed a tool that fully implements all the stages of the methodology.