A Multi-Agent System for Modelling Carbohydrate Oxidation in Cell  Flavio Corradini, Emanuela Merelli, and Marco Vita Universit` a di Camerino, Dipartimento di Matematica e Informatica Camerino, 62032, Italy, {flavio.corradini,emanuela.merelli,marco.vita}@unicam.it Abstract. A cell consists of a large number of components interact- ing in a dynamic environment. The complexity of interaction among cell components and functions makes design of cell simulations a challenging task for biologists. We posit that the paradigm of agent-oriented soft- ware engineering (AOSE), in which complex systems are organized as autonomous software entities (agents) situated in an environment and communicating via high-level languages and protocols (ontologies), may be a natural approach for such models. To evaluate this approach, we constructed a model of cell components involved in the metabolic path- way of carbohydrate oxidation. The agent-oriented organization proved natural and useful in representing three different views of the cell system (functional, dynamic, and static structural) and in supporting bioscien- tists querying a system very close to their mental model. 1 Introduction A biological cell is a complex system. It consists of a large number of components interacting with each other to perform cell functions. Each cell is a self-contained and self-maintaining entity: It can take in nutrients, convert these nutrients into energy, carry out specialized functions, and reproduce itself. The modelling and simulation of cell behaviour belongs to an emerging research area, Systems Biology [7], whose aim is to understand how biological systems function, by studying at different abstraction levels the relationships and interactions between various parts of a biological system, e.g. organelles, cells, physiological systems, organisms etc., and producing a model as close as possible to the biological reality. The modelling of complex systems, as suggested in Kitano [7], implies a deep understanding of the biological system both in terms of its structure and its behaviour. Cells grow through the functioning of cell metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. In particular, carbohydrate oxidation is the process by which a cell produces  This work was supported by Center of Excellence for Research ‘DEWS: Architectures and Design Methodologies for Embedded Controllers, Wireless Interconnect and System-on-chip’ and Italian CIPE project ’Sistemi Cooperativi Multiagente’. Work completed while the second author was on Fulbright leave at University of Oregon.