title: Automatic analysis of computation in biochemical reactions.
abstract: We propose a modeling and analysis method for biochemical reactions based on finite state automata. This is a completely different approach compared to traditional modeling of reactions by differential equations. Our method aims to explore the algebraic structure behind chemical reactions using automatically generated coordinate systems. In this paper we briefly summarize the underlying mathematical theory (the algebraic hierarchical decomposition theory of finite state automata) and describe how such automata can be derived from the description of chemical reaction networks. We also outline techniques for the flexible manipulation of existing models. As a real-world example we use the Krebs citric acid cycle.
authors.affiliation: The Royal Society, Wolfson Foundation BioComputation Laboratory & Algorithms Research Group, Centre for Computer Science and Informatics Research, University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom. A.Egri-Nagy@herts.ac.uk
authors.forename: Attila
authors.initials: A
authors.lastname: Egri-Nagy
authors.forename: Chrystopher L
authors.initials: CL
authors.lastname: Nehaniv
authors.forename: John L
authors.initials: JL
authors.lastname: Rhodes
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Schilstra
mesh_terms: D001669:Biochemical Phenomena; D002952:Citric Acid Cycle; D019295:Computational Biology / Q000379:methods*; D008956:Models, Chemical