The term network is more and more widespread in all the fields of human investigation from physics to sociology. It evokes a systemic approach to problems able to overcome the limitations reductionist approaches have evidenced for some decades. Network-based approaches gave very brilliant results in fields like biochemistry, where the consideration of the whole set of metabolic reactions of an organism allowed us to understand some very important properties of the organisms that cannot be appreciated by the simple enumeration of single biochemical reactions. Nevertheless, the lack of consciousness that networks are modeling tools and not real entities could be detrimental to the exploitation of the full potential of this paradigm. Some applications of network-based modeling will be presented to both introduce the basic terminology of the emergent network paradigm and highlight strengths and limitations of the method.