Cell modeling with reusable agent-based formalisms

Biologists are building increasingly complex models and simulations of cells and other biological entities, and are looking at alternatives to traditional representations. Making use of the object-oriented (OO) paradigm, the Unified Modeling Language (UML) and Real-time Object-Oriented Modeling (ROOM) visual formalisms, and the Rational Rose RealTime (RRT) visual modeling tool, we summarize a previously-described multi-step process for constructing top-down models of cells. We first construct a simple model of a cell using an architecture in which all objects are containers, agents, or passive objects. We then reuse these architectural principles and components to extend our simple cell model into a more complex cell, the goal being to demonstrate that encapsulation familiar to artificial intelligence researchers can be employed by systems biologists in their models. A red blood cell is embedded in a straight-forward manner within a larger system, which is in turn iteratively embedded within still larger systems, including a blood vessel, a circulatory system, a human being, and a simple ecology. Each complexity increment reuses the same architectural principles, including the use of agents, each of which continuously either moves passive small molecules between containers, or transforms these passive objects from one type into another. We show how it is possible to start with a direct diagrammatic representation of a biological structure such as a cell, using terminology familiar to biologists, and by following a process of gradually adding more and more detail, arrive at a system with structure and behavior of arbitrary complexity that can run and be observed on a computer.