T (2004) Cell Modeling using Agent-based Formalisms

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.