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
Visual modeling with Rational Rose and UML
Visual modeling with Rational Rose and UML
The Rational Unified Process: An Introduction, Second Edition
The Rational Unified Process: An Introduction, Second Edition
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
Combining analysis and synthesis in a model of a biological cell
Proceedings of the 2004 ACM symposium on Applied computing
Unified Modeling Language Reference Manual, The (2nd Edition)
Unified Modeling Language Reference Manual, The (2nd Edition)
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
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Engineering Self-modeling Systems: Application to Biology
Engineering Societies in the Agents World IX
Modeling Biology using Generic Reactive Animation
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Flexible case-based retrieval for comparative genomics
Applied Intelligence
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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.