An agent-based approach for building complex software systems
Communications of the ACM
Agent-oriented software engineering: the state of the art
First international workshop, AOSE 2000 on Agent-oriented software engineering
Challenges and Research Directions in Agent-Oriented Software Engineering
Autonomous Agents and Multi-Agent Systems
Abstract machines of systems biology
Transactions on Computational Systems Biology III
Hermes: agent-based middleware for mobile computing
SFM-Moby'05 Proceedings of the 5th international conference on Formal Methods for the Design of Computer, Communication, and Software Systems: mobile computing
A&A for modelling and engineering simulations in Systems Biology
International Journal of Agent-Oriented Software Engineering
On the use of organisation modelling techniques to address biological organisation
Multiagent and Grid Systems - Multi-agent systems for medicine, computational biology, and bioinformatics
Validating MAS simulation models with mutation
Multiagent and Grid Systems - Multi-agent systems for medicine, computational biology, and bioinformatics
| Hi-index | 0.00 |
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.