Organisms. Computational biology

Abstract In this paper, the agent-oriented modeling per-spective to cope with biological complexity is discussed. Three levels of dynamics can distinguished and related to each other: dynamics of externally observable agent behav-ior, dynamics of internal agent processes, and dynamics of multi-agent organisations. This paper addresses the first two. Basic agent concepts to describe externally observable agent behavior are introduced. In the context of 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 con-cepts are illustrated for specification of dynamic properties in the two case studies. Furthermore, the relationships be-tween dynamic properties of externally observable behavior and dynamic properties of internal agent processes are ad-dressed and illustrated for the animal and cell case studies