Title: A&A for modelling and engineering simulations in Systems Biology

Authors: Sara Montagna, Alessandro Ricci, Andrea Omicini

Addresses: Alma Mater Studiorum–Universita di Bologna, via Venezia 52, 47023, Cesena, Italy. ' Alma Mater Studiorum–Universita di Bologna, via Venezia 52, 47023, Cesena, Italy. ' Alma Mater Studiorum–Universita di Bologna, via Venezia 52, 47023, Cesena, Italy

Abstract: Systems Biology (SB) promotes a system-level understanding of biological systems, and requires modelling and simulation tools for analysing biological systems dynamics. The articulation of Multiagent Systems (MASs) in terms of multiple, distributed and autonomous computational entities makes MAS a seemingly fit paradigm in SB. In this paper we adopt the Agents and Artefacts (A&A) metamodel where the notions of agent, artefact and workspace are taken as the basic bricks for MASs as the ontological foundation for our Multiagent-based Simulation (MABS) framework, and discuss how this impacts on SB. After recasting the A&A abstractions within the domain and design models, we specialise A&A within the SB context, and show an operational model based on the TuCSoN agent coordination infrastructure, upon which our simulation framework is implemented. As a case study, we model the well-studied metabolic pathway of 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.

DOI: 10.1504/IJAOSE.2008.017316

International Journal of Agent-Oriented Software Engineering, 2008 Vol.2 No.2, pp.222 - 245

Available online: 26 Feb 2008 *

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