Agent-Oriented Modeling of the Dynamics of Complex Biological Processes I: Single Agent Models

In the pair of papers of which this is Part I, the agent-oriented modeling perspective to cope with biological complexity is discussed. Three levels of dynamics are distinguished and related to each other: dynamics of externally observable agent behavior, dynamics of internal agent processes, and dynamics of multi-agent organisations. Basic agent concepts to describe externally observable agent behavior are introduced. In the context of the two case studies on animal behavior and cell functioning, it is shown how these concepts can be used to specify dynamic properties. In addition, a number of basic agent concepts to describe an agent’s internal processes are introduced. Also these concepts are illustrated for specification of dynamic properties in the two case studies. Furthermore, the relationships between dynamic properties of externally observable behavior and dynamic properties of internal agent processes are addressed and illustrated for the animal and cell case studies. In the second paper, Part II, the dynamics within an organisation of multiple agents are addressed. Associated to the organisational structure, dynamic properties at different levels of aggregation are presented, related to each other, and illustrated for a third case study: the organisation of the circulatory system in mammals.