In this communication we introduce a general framework and discussion on the role of models and the modelling process within the scientific activity in the biosciences realm. The objective is sum up the common procedure during the formalization and analysis of a biological problem under the foundations of Systems Biology, which approach the study of biological systems as a whole.We begin by presenting the definitions of (biological) system and model. Particular attention is given to the meaning of mathematical model within the context of the biology. Then, we present the modelization and analysis process of biological systems. Three stages are described in detail: conceptualization of the biological system into a model, mathematical formalization of the previous conceptual model and optimization and system management derived from the analysis of the mathematical model.All along this presentation the main features and shortcomings of the process are developed together with a set of rules that could help in the modelling endeavour of any biological system. Special regard is given to the formative requirements and the interdisciplinary nature of this approach. We conclude with some general considerations on the challenges that the modelling are currently posing to the current biology
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