Overview: A core challenge in studying pulmonary tuberculosis or its treatment is heterogeneity. Multiple granulomas, complex and often treatment-resistant immune structures, form in the lungs of hosts infected with pulmonary Mtb. A single host will have multiple granulomas, and each granuloma within that host will have distinct dynamics. Moreover, we see differences in TB progression between hosts as well. For this, we have developed HostSim, a multi-scale whole-host model of Mtb infection. While the paper associated with this webpage details the implementation of drug treatment of antibiotic-susceptible Mtb infection, there are a plethora of cellular and molecular interactions that underpin granuloma foundation, maturation, and dissemination - each represented by equations or inter-compartmental exchanges detailed in this online appendix. Each of these mechanisms is also parameterized, and our parameter ranges are also found in this digital appendix.