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

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Journal of Simulation 7(3), pages 216–226
August 2013

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.

keywordsSimulation; Intracellular signalling pathways; Computational biology; Self-organising coordination; Tuple-based models.
journal or series
book Journal of Simulation (JOS)