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We summarize and transfer state-of-the art approaches from other fields like Systems Biology to infectious disease models. For this purpose, we use a simple SIR model with data from an influenza outbreak at an English boarding school in 1978 and a more complex model of a vector-borne disease with data from the Zika virus outbreak in Colombia in 2015\u20132016. Besides parameter estimation using a deterministic multistart optimization approach, a multitude of analyses based on the profile likelihood are presented comprising identifiability analysis and model reduction. 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