Fig 1. Overall structure of the model.

Schema representing the arrangement of models at three spatial scales. Cells are represented by discrete, autonomous agents that can differentiate into different subtypes, divide, and die. Each cell contains a constraint-based metabolic model for each phenotype and a logical model of signaling and gene regulatory pathways. The agents themselves reside in and travel between three isotropic compartments. Each compartment is associated with a set of cytokine concentrations, modeled by ordinary differential equations, that affect and are affected by the agents.