Table 1. Summary of agents, data layers, and their interactions encoded in the ABM.

Substances in ABM	Cell Sources in ABM	Biological Functions in ABM
DAMPs	secreted by damaged Tissue cells	Chemo-attract and Activate Neutrophils
TNF-α	secreted by Activated Neutrophils	Chemo-attract resting and M1 Macrophages, activate Macrophages to M1 state
IL-1β	secreted by M1 Macrophages	Chemo-attract resting and M1 Macrophages, activate Macrophages to M1 state, at high levels activate Macrophages to M2 state
TGF-β1	secreted by M2 Macrophages	Chemo-attract resting and M2 Macrophages, activate Macrophages to M2 state
ROS	secreted by Tissue Cells on Reperfusion, by Neutrophils on death	Injure Tissue Cells
Oxidase	produced inside Tissue Cells during Ischemia	React with Oxygen to produce ROS
Oxygen	released by Blood Vessels	Necessary for Tissue Cell health, react with Oxidase to produce ROS

Substances are all encoded as Data Layers; Cells are all encoded as Agents, each with its own type. See Fig 1B for schematic.