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

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

Pedro Pablo González Pérez, Andrea Omicini, Marco Sbaraglia
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.
Keywords: Simulation; Intracellular signalling pathways; Computational biology; Self-organising coordination; Tuple-based models.
Journal of Simulation 7(3), pages 216-226, August 2013.
Giancarlo Fortino, Michael J. North (eds.), Palgrave Macmillan
Special Issue: Agent-based Modeling and Simulation
@article{btssoc-jos7,
	Author = {Gonz{\'a}lez P{\'e}rez, Pedro Pablo and Omicini, Andrea and Sbaraglia, Marco},
	Doi = {10.1057/jos.2012.28},
	Editor = {Fortino, Giancarlo and North, Michael J.},
	Issn = {1747-7778},
	Issn-Online = {1747-7786},
	Journal = {Journal of Simulation},
	Keywords = {Simulation; Intracellular signalling pathways; Computational biology; Self-organising coordination; Tuple-based models.},
	Month = aug,
	Note = {Special Issue: Agent-based Modeling and Simulation},
	Number = 3,
	Pages = {216--226},
	Publisher = {Palgrave Macmillan},
	ScopusId = {2-s2.0-84880868530},
	Title = {A Biochemically-inspired Coordination-based Model for Simulating Intracellular Signalling Pathways},
	Url = {http://www.palgrave-journals.com/jos/journal/v7/n3/full/jos201228a.html},
	Url-Pdf = {http://www.palgrave-journals.com/jos/journal/v7/n3/pdf/jos201228a.pdf},
	Volume = 7,
	WosId = {000322750000007},
	Year = 2013}