Model refinement through high-performance computing: an agent-based HIV example

Immunome Research

Table 2 Agent population dynamics

Variations	Viral agents	CD4 agents	CD8 agents	APC agents
Increases	Production by infected CD4	Created in thymus, or produced by multiplicating agent	Created in thymus, or produced by multiplicating agent	New agent created
Decreases	Agent ingested by APC, or infecting CD4	Infected agent destroyed, or end of life	End of immune response, or end of life	Presenting agent destroyed, or end of life

At the start of a simulation, initial agent populations are specified in a parameterisation file. Agent populations then dynamically evolve, following specific rules as when agents may be created or destroyed.