Statecharts: A visual formalism for complex systems
Science of Computer Programming
Communications of the ACM
Real-time object-oriented modeling
Real-time object-oriented modeling
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
A multi-agent system for the quantitative simulation of biological networks
AAMAS '03 Proceedings of the second international joint conference on Autonomous agents and multiagent systems
A grand challenge: full reactive modeling of a multi-cellular animal
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
The Knowledge Engineering Review
Formal Validation of Asynchronous Interaction-Agents Algorithms for Reaction-Diffusion Problems
Proceedings of the 21st International Workshop on Principles of Advanced and Distributed Simulation
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
On the use of organisation modelling techniques to address biological organisation
Multiagent and Grid Systems - Multi-agent systems for medicine, computational biology, and bioinformatics
A Hybrid Agent-Based Model of Chemotaxis
ICCS '07 Proceedings of the 7th international conference on Computational Science, Part I: ICCS 2007
EPIA'05 Proceedings of the 12th Portuguese conference on Progress in Artificial Intelligence
Multi-agent model of hepatitis C virus infection
Artificial Intelligence in Medicine
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The systems biology community is building increasingly complex models and simulations of cells and other biological entities. This community is beginning to look at alternatives to traditional representations such as those provided by ordinary differential equations (ODE). Making use of the object-oriented (OO) paradigm, the Unified Modeling Language (UML) and Real-time Object-Oriented Modeling (ROOM) visual formalisms, we describe a simple model that includes membranes with lipid bilayers, multiple compartments including a variable number of mitochondria, substrate molecules, enzymes with reaction rules, and metabolic pathways. We demonstrate the validation of the model by comparison with Gepasi and comment on the reusability of model components.