Designing models of complex phenomena is a difficult task in engineering that can be tackled by composing a number of partial models to produce a global model of the phenomena. We propose to embed the partial models in software agents and to implement their composition as a cooperative negotiation between the agents. The resulting multiagent system provides a global model of a phenomenon. We applied this approach in modelling two complex physiological processes: the heart rate regulation and the glucose-insulin metabolism. Beyond the effectiveness demonstrated in these two applications, the idea of using models associated to software agents to give reason of complex phenomena is in accordance with current tendencies in epistemology, where it is evident an increasing use of computational models for scientific explanation and analysis. Therefore, our approach has not only a practical, but also a theoretical significance: agents embedding models are a technology suitable both to representing and to investigating reality.