This article proposes a generic modeling approach of systems of systems (SoS) using agent-based modeling (ABM). SoSs are large scale systems including numerous-possibly heterogeneous-interacting component systems (CS) evolving in a dynamic environment. The aim of this article is to provide generic formalism allowing to represent and control the whole complexity of a SoS using agent-based simulations. Models generated using this formalism encompass static and dynamic aspects of SoSs. They consider reorganization of SoSs caused by changes of goals or subsystem capacity. All these elements are illustrated in this article using a SoS case study of Intelligent Automated Vehicles (IAV) initiated by the InTraDE (Intelligent Transportation for Dynamic Environment) European project to automate the port container logistic.