Object oriented programming: an evolutionary approach
Object oriented programming: an evolutionary approach
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
The Unified Modeling Language reference manual
The Unified Modeling Language reference manual
The Creatures global digital ecosystem
Artificial Life
Towards the Implementation of Evolving Autopoietic Artificial Agents
ECAL '01 Proceedings of the 6th European Conference on Advances in Artificial Life
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
Cell modeling with reusable agent-based formalisms
Applied Intelligence
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
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We have previously described a top-down analytical approach, Cell Assembly Kit (CellAK), based on the object-oriented (OO) paradigm and the Unified Modeling Language (UML) and Real-Time Object-Oriented Methodology (ROOM) formalisms, for developing models and simulations of cells and other biological entities. In this approach, models consist of a hierarchy of containers (ex: cytosol), active objects with behavior (ex: enzymes, lipid bilayers, transport proteins), and passive small molecules (ex: glucose, pyruvate). In this paper we describe the Substrate Catalyst Link (SCL) bottom-up synthesis approach [17], the concept of autopoiesis on which it is based, and what we have learned in trying to integrate this approach into CellAK. The enhanced CellAK architecture consists of a network of active objects (polymers), each of which has behavior that causally depends partly on its own fine-grained structure (monomers), where this structure is constantly changing through interaction with other active objects.