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A transportation system is spatially and functionally distributed; its subsystems have a high degree of autonomy and are in constant interaction with each other and with the surrounding geographic environment. Modeling and simulating such systems in large-scale geographic spaces is a complex process. In this paper we address the domain of railway systems, and more particularly the problem of detecting risky areas along railroads. This requires that we consider a variety of static and dynamic variables, including train characteristics, hazardous events (e.g. rock-falls), and the properties of the large-scale geographic environment, as well as weather conditions. This simulation enables us to recommend speed limits in risky areas while taking into account all of the aforementioned factors. Since statistical and analytical models are not appropriate to represent such a complex process in which spatial constraints are of high importance, we adopted a multi-agent geo-simulation (MAGS) approach that facilitates the simulation of complex systems in large-scale geo-referenced environments. In this paper, we present Train-MAGS, an agent-based geo-simulation tool that simulates train behaviors in risky areas in large-scale virtual geographic environments. We also demonstrate how risky areas can be detected in real time using an agent-based approach. This work also illustrates how the application of artificial intelligence techniques, such as the MAGS approach, provides interesting perspectives of realistic and plausible simulations aimed at improving the functioning, the efficiency, and the safety of the transportation systems.