The modeling framework used in this work is based on a shelf-scale model recently presented by the authors for the freezing stage of the freeze-drying process in vials. We refer to the original work for a detailed derivation of the model from first principles and present in section 2.1 a summary of the relevant equations and of the underlying principles. In section 2.2 we discuss how to interpret the model predictions and how to quantify batch heterogeneity. Section 2.3, finally, outlines the experimental methods.