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This paper presents methods for the parameter identification of a model of subtilin production by Bacillus subtilis. Based on a stochastic hybrid model, identification is split in two subproblems: estimation of the genetic network regulating subtilin production from gene expression data, and estimation of population dynamics based on nutrient and population level data. Techniques for identification of switching dynamics from sparse and irregularly sampled observations are developed and applied to simulated data. Numerical results are provided to show the effectiveness of our methods.