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Bioinformatics Advance Access published online on May 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti502
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 1, 2005
Revised May 6, 2005
Accepted May 13, 2005

Applications note

MFAML: a standard data structure for representing and exchanging metabolic flux models

Hongseok Yun 1, Dong-Yup Lee 2, Joonwoo Jeong 1, Seunghyun Lee 1, and Sang Yup Lee 2*

1 Bioinformatics Research Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea
2 Bioinformatics Research Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Department of BioSystems, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea

* To whom correspondence should be addressed.
Sang Yup Lee, E-mail: leesy{at}kaist.ac.kr


  Abstract

Summary: MFAML is a standard data structure designed for the formal representation and effective exchange of metabolic flux models. It allows for the explicit description of stationary states of a metabolic system by defining environmental/genetic conditions of the system, e.g., flux measurements, balancing constraints and physiological objectives as well as basic information on metabolites and reactions. In addition, a library of MFAML comprising a model parser and a converter provides an open framework for establishing the pipeline from metabolic modeling to metabolic flux analysis.

Availability: MFAML (version 1) is fully described and available at http://mbel.kaist.ac.kr/mfaml/.


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