A biochemically inspired coordination-based model for simulating intracellular signalling pathways

P P González Pérez, A Omicini and M Sbaraglia

Journal of Simulation, 2013, vol. 7, issue 3, 216-226

Abstract: 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 the 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 for self-organising coordination, 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.

Date: 2013
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DOI: 10.1057/jos.2012.28

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