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A&A for Modelling and Engineering Simulations in Systems Biology

Sara Montagna, Alessandro Ricci, Andrea Omicini
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
International Journal of Agent-Oriented Software Engineering 2(2), pages 222-245, 2008.
Massimo Cossentino, Giancarlo Fortino, Wilma Russo (eds.), Inderscience Publishers
Special Issue on Multi-Agent Systems and Simulation 
@article{simulation-ijaose2,
	Author = {Montagna, Sara and Ricci, Alessandro and Omicini, Andrea},
	Doi = {10.1504/IJAOSE.2008.017316},
	Editor = {Cossentino, Massimo and Fortino, Giancarlo and Russo, Wilma},
	Issn = {1746-1375},
	Issn-Online = {1746-1383},
	Journal = {International Journal of Agent-Oriented Software Engineering},
	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},
	Note = {Special Issue on Multi-Agent Systems and Simulation},
	Number = 2,
	Pages = {222--245},
	Publisher = {Inderscience Publishers},
	ScopusId = {2-s2.0-79956135898},
	Title = {{A\&A} for Modelling and Engineering Simulations in {S}ystems {B}iology},
	Url = {http://www.inderscience.com/search/index.php?action=record&rec_id=17316},
	Volume = 2,
	Year = 2008}