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

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.

Keywords:

• simulation
• intracellular signalling pathways
• computational biology
• self-organising coordination
• tuple-based models

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.