A Biochemically-inspired Coordination-based Model for Simulating Intracellular Signalling Pathways

Modelling the interaction among system components is a fundamental issue in complex system simulation. Simulation frameworks based on coordination models — that is, explicitly handling interaction — suit well complex system simulation: and those based on nature-inspired coordination models, in particular, are well-suited for the simulation of complex natural systems.
In this paper we adopt an approach to self-organising coordination based on biochemical tuple spaces (BTS-SOC), and show how it can be applied to the simulation of complex interaction patterns of intracellular signalling pathways. We first present the model and a general high-level architecture, then we develop and discuss a simple case study—a single signalling pathway from the complex network of the Ras signalling pathways.