AGENT-BASED MODELLING FOR SYSTEMS BIOLOGY

 

The Basics

Mediation

Pro-Active / Reactive Agents

Adaptive / Non-Adaptive Agents

Organisational Metaphors

Situated and Mobile Agents

Mediation of Interactions

 

Mediation

Interactions between agents and their environment need not be direct. Instead, they can be mediated . Mediated interactions are those that take place via some intermediate system component such as another component or environmental substrate called a mediator or mediating artifact . For example, when an agent communicates with another agent, a set of conditions may need to be met (the protocol ) for the "message" to be transmitted; the mediating artifact ensures that this happens and only allows communication to take place when the conditions have been met.

Mediating Artefacts

Mediating Artefacts can be understood in terms of metaphors borrowed from working organisations. Coordinating artefacts for example, are those that govern the cooperative actions of a set of agents contributing to a particular task. Mediating artefacts are defined relative to a particular interaction relationship and only exist for as long as this relationship holds.

For example, say a type of molecule, A is the catalyst for a reaction between molecule types B and C . In a simulation, A will only perform the role of catalyst (a mediating role) when it encounters instances of B and C at the same time. For the rest of the time, it may perform other roles and follow its own sets of behavioural rules that are unrelated to the reaction between B and C . A is the mediator for the interaction, in this case a reaction, between B and C .

Next: Proactive and Reactive Agents

 

© 2006 Chih-Chun Chen, Christopher D. Clack, Sylvia Nagl