Much research in ABM has focused on finding suitable metaphors that best support the structure of the systems being modelled. These have tended to be based on commercial organisations. ABM offers a means of coping with the structural complexity of biological systems. Importantly, it allows different aspects of biological entities to be expressed and enables them to play several different roles at the same time. An entity, A can at one time be participating in a chemical reaction, acting as a physical obstacle to entity B, and moving away from high concentrations of C. This can be done using the Agent-Group-Role (AGR) formalism, which is based on a hierarchical organisational structure.

In the AGR formalism, agents have roles. A role has a set of properties (state variables) and behavioural capabilities (rules) associated with it but has no independent existence apart from the agents that instantiate it.

Roles can be grouped into separate modules representing sub-systems in their own right. For example, different reaction and signalling pathways can be represented by different groups. These groups can also interact with one another, and entities can participate in different groups at the same time. This formalism models well the independence, inter-dependency, and concurrency of different sub-systems or sub-models in models of biological systems.

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