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

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Journal of Simulation

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.

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Acknowledgements

We would like to thank Sara Montagna for her invaluable contribution in organising our early activity on this paper. This work has been partially supported by the EU-FP7-FET Proactive project SAPERE—Self-aware Pervasive Service Ecosystems, under contract no. 256873.

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Authors and Affiliations

  1. Universidad Autónoma Metropolitana, Mexico city, Mexico

    P P González Pérez

  2. Alma Mater Studiorum—Università di Bologna, Bologna/Cesena, Italy

    A Omicini & M Sbaraglia

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  1. P P González Pérez
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  2. A Omicini
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  3. M Sbaraglia
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Correspondence to A Omicini.

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González Pérez, P., Omicini, A. & Sbaraglia, M. A biochemically inspired coordination-based model for simulating intracellular signalling pathways. J Simulation 7, 216–226 (2013). https://doi.org/10.1057/jos.2012.28

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