Corradini, Flavio and Merelli, Emanuela and Vita, Marco
A Multi-Agent System for Modelling Carbohydrate Oxidation in Cell.
Lecture Notes in Computer Science, 3481.
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A cell consists of a large number of components interacting
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 software
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 pathway
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 bioscientists
querying a system very close to their mental model.
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