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The application areas for plastic optical fibers such as in-building or aircraft networks usually have tight power budgets and require multiple passive components. In addition, advanced modulation formats are being considered for transmission over plastic optical fibers (POFs) to increase spectral efficiency. In this scenario, there is a clear need for a flexible and dynamic system-level simulation framework for POFs that includes models of light propagation in POFs and the components that are needed to evaluate the entire system performance. Until recently, commercial simulation software either was designed specifically for single-mode glass fibers or modeled individual guided modes in multimode fibers with considerable detail, which is not adequate for large-core POFs where there are millions of propagation modes, strong mode coupling and high variability. These are some of the many challenges involved in the modeling and simulation of POF-based systems. Here, we describe how we are addressing these challenges with models based on an intensity-vs-angle representation of the multimode signal rather than one that attempts to model all the modes in the fiber. Furthermore, we present model approaches for the individual components that comprise the POF-based system and how the models have been incorporated into system-level simulations, including the commercial software packages SimulinkTM and ModeSYSTM.