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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth125
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 16, 2003
Revised December 16, 2003
Accepted December 29, 2003

Applications note

A general computational model of mitochondrial metabolism in a whole organelle scale

Katsuyuki Yugi 1 Masaru Tomita 1*

1 Institute for Advanced Biosciences, Keio University, Endo 5322, Fujisawa, Kanagawa, 252-8520, Japan

* To whom correspondence should be addressed. E-mail: chaos{at}e-cell.org.


  Abstract

Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of ECell2, a publicly available simulation system. The general model consists of 58 enzymatic reactions and 117 metabolites, representing the respiratory chain, the TCA cycle, the fatty acid {beta}-oxidation, and the inner-membrane transport system. It is based on previously published enzyme kinetics studies in the literature; we have successfully integrated and packaged them into a single large model. The model can be easily extended and modified so that mitochondrial biologists/physiologists can integrate their own models and evaluate them in the context of the whole organelle metabolism.

Availability: The mitochondrial model is bundled up with E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. The CD-ROMs are also available and distributed at major conferences.

Supplementary Information: All the kinetic data are available via http://www.e-cell.org.


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