A&A for Modelling and Engineering Simulations in Systems Biology


Sara Montagna, Alessandro Ricci, Andrea Omicini

International Journal of Agent-Oriented Software Engineering 2(2), pages 222–245
2008

Systems Biology promotes a system-level understanding of biological systems, and requires modelling and simulating tools for understanding, controlling and re-creating biological systems and their dynamics. The articulation of multiagent systems (MAS) in terms of multiple, distributed and autonomous computational entities makes MAS a seemingly fit paradigm for modelling and simulating biological systems and networks according to the System Biology perspective.

In this paper we adopt the  A&A (agents and artifacts) meta-model – where the notions of agent, artifact, and workspace are taken as the basic bricks for MAS – as the ontological foundation for our multi-agent-based simulation (MABS) framework, and discuss how this impacts on the modelling and simulation of biological systems. After re-casting the A&A abstractions within the domain and design models, we specialise A&A within the System Biology context, and show a possible operational model based on the TuCSoN agent coordination infrastructure, upon which our simulation framework is implemented. There, agents – representing active biological components such as proteins – interact by means of artifacts built upon TuCSoN tuple centres – representing the bio-chemical environment that enables, mediates and govern the interaction of biological components – within workspaces—representing different spatial regions, like cell compartments. As a case study, we model and simulate a well-studied metabolic pathway such as glycolysis, and present some results of the simulation.

(keywords) Systems biology; multiagent-based simulation; MABS; A&A metamodelling; MAS engineering; TuCSoN; multi-agent systems; agent-based systems; agents and artefacts; system dynamics; metabolic pathway; glycolysis

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Publication

— authors

— editors

Massimo Cossentino, Giancarlo Fortino, Wilma Russo

— status

published

— sort

article in journal

— publication date

2008

— journal

International Journal of Agent-Oriented Software Engineering

— volume

2

— issue

2

— pages

222–245

URLs

original page

identifiers

— DOI

10.1504/IJAOSE.2008.017316

— ACM

10.1504/IJAOSE.2008.017316

— IRIS

11585/62493

— Scopus

2-s2.0-79956135898

— print ISSN

1746-1375

— online ISSN

1746-1383

notes

— note

Special Issue on Multi-Agent Systems and Simulation

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