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Modeling and simulation of intracellular biochemical networks is a critical method to study the biological system behaviors. The phenomena of self organization play a crucial role in biological systems and Agent-based modeling (ABM) has been widely viewed as a computational framework to study the complex systems. Agent-based modeling approach has tremendous potential in advancing studying the phenomena of self-organization in biochemical networks, but is still under-utilized both in theory and practice. In this study we present a new bottom-up computational modeling and simulation paradigm-Agent Based Modeling (ABM) with Reaction Agents (ABM-RA) which models the biochemical networks based on self organization and is a mathematical formalization of a multi-agent system for the biochemical reaction networks. Experiment results show that ABM-RA is a generic approach. It is thus a fundamentally better fit to a real biological system than the top-down approach which relies heavily on human abstractions.
Intelligent Computation Technology and Automation (ICICTA), 2011 International Conference on (Volume:1 )
Date of Conference: 28-29 March 2011