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}

    

Publication

— authors

Pedro Pablo González Pérez, Andrea Omicini, Marco Sbaraglia

— editors

Giancarlo Fortino, Michael J. North

— status

published

— sort

article in journal

Venue

— journal

Journal of Simulation

— volume/issue

7 (3)

— publication date

August 2013

— pages

216-226

URLs & IDs

original page
original PDF

— DOI

10.1057/jos.2012.28

— IRIS

11585/256517

— Scopus

2-s2.0-84880868530

— WoS / ISI

000322750000007

— print ISSN

1747-7778

— online ISSN

1747-7786

BibTeX

— BibTeX ID
btssoc-jos7
— BibTeX category
article

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