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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti068
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 23, 2004
Revised September 16, 2004
Accepted September 17, 2004

Article

An enzyme mechanism language for the mathematical modeling of metabolic pathways

Chin-Rang Yang 1, Bruce E. Shapiro 2, Eric D. Mjolsness 3, and G. Wesley Hatfield 1*

1 Department of Microbiology and Molecular Genetics, College of Medicine, Irvine, California 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697, USA
2 Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, USA
3 School of Information and Computer Science, Irvine, California 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697, USA

* To whom correspondence should be addressed.
G. Wesley Hatfield, E-mail: gwhatfie{at}uci.edu


  Abstract

Motivation: As a first step towards the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways.

Results: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association-dissociation reactions that are translated by Cellerator into ordinary differential equations (ODEs) that are numerically solved by MathematicaTM. Also, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.

Availability: A MathematicaTM executable kMech.m file is available at the University of California, Irvine, Institute for Genomics and Bioinformatics website, http://www.igb.uci.edu/servers/sb.html. Cellerator, free of charge to academic, U.S. government, and other nonprofit organizations, can be obtained at the Cellerator web site, http://www-aig.jpl.nasa.gov/public/mls/cellerator/feedback.html.

Supplementary Information: http://www.igb.uci.edu/servers/sb.html.


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