Experimental design and computational model.

(A) Experimental design for data collection and measurement on the 28 Non-Human Primate. All the datasets are available online as Supporting Information (S2S6 Tables). (B) Schematic representing the three compartments captured by our computational model. The emphasis is on describing all the lymphocyte phenotypes (both CD4+ and CD8+) tracked during the analysis. The cells populate three different compartments/organs: lung, lymph node and blood. The lung is modeled as an Agent-Based Model (ABM), while the blood and the lymph node are modeled as an Equation-Based Model (EBM), namely as an Ordinary Differential Equation (ODE) system. For most of the phenotypes, both Mtb-specific (colored) and non Mtb-specific (grey) cells are tracked. APC: represented as a proxy in the computational model (see Materials and Methods section and S1 and S2 Texts for details).