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New time-scale criteria for model simplification of bio-reaction systems

BACKGROUND: Quasi-steady state approximation (QSSA) based on time-scale analysis is known to be an effective method for simplifying metabolic reaction system, but the conventional analysis becomes time-consuming and tedious when the system is large. Although there are automatic methods, they are bas...

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Autores principales: Choi, Junwon, Yang, Kyung-won, Lee, Tai-yong, Lee, Sang Yup
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553091/
https://www.ncbi.nlm.nih.gov/pubmed/18694523
http://dx.doi.org/10.1186/1471-2105-9-338
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author Choi, Junwon
Yang, Kyung-won
Lee, Tai-yong
Lee, Sang Yup
author_facet Choi, Junwon
Yang, Kyung-won
Lee, Tai-yong
Lee, Sang Yup
author_sort Choi, Junwon
collection PubMed
description BACKGROUND: Quasi-steady state approximation (QSSA) based on time-scale analysis is known to be an effective method for simplifying metabolic reaction system, but the conventional analysis becomes time-consuming and tedious when the system is large. Although there are automatic methods, they are based on eigenvalue calculations of the Jacobian matrix and on linear transformations, which have a high computation cost. A more efficient estimation approach is necessary for complex systems. RESULTS: This work derived new time-scale factor by focusing on the problem structure. By mathematically reasoning the balancing behavior of fast species, new time-scale criteria were derived with a simple expression that uses the Jacobian matrix directly. The algorithm requires no linear transformation or decomposition of the Jacobian matrix, which has been an essential part for previous automatic time-scaling methods. Furthermore, the proposed scale factor is estimated locally. Therefore, an iterative procedure was also developed to find the possible multiple boundary layers and to derive an appropriate reduced model. CONCLUSION: By successive calculation of the newly derived time-scale criteria, it was possible to detect multiple boundary layers of full ordinary differential equation (ODE) models. Besides, the iterative procedure could derive the appropriate reduced differential algebraic equation (DAE) model with consistent initial values, which was tested with simple examples and a practical example.
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spelling pubmed-25530912008-09-25 New time-scale criteria for model simplification of bio-reaction systems Choi, Junwon Yang, Kyung-won Lee, Tai-yong Lee, Sang Yup BMC Bioinformatics Methodology Article BACKGROUND: Quasi-steady state approximation (QSSA) based on time-scale analysis is known to be an effective method for simplifying metabolic reaction system, but the conventional analysis becomes time-consuming and tedious when the system is large. Although there are automatic methods, they are based on eigenvalue calculations of the Jacobian matrix and on linear transformations, which have a high computation cost. A more efficient estimation approach is necessary for complex systems. RESULTS: This work derived new time-scale factor by focusing on the problem structure. By mathematically reasoning the balancing behavior of fast species, new time-scale criteria were derived with a simple expression that uses the Jacobian matrix directly. The algorithm requires no linear transformation or decomposition of the Jacobian matrix, which has been an essential part for previous automatic time-scaling methods. Furthermore, the proposed scale factor is estimated locally. Therefore, an iterative procedure was also developed to find the possible multiple boundary layers and to derive an appropriate reduced model. CONCLUSION: By successive calculation of the newly derived time-scale criteria, it was possible to detect multiple boundary layers of full ordinary differential equation (ODE) models. Besides, the iterative procedure could derive the appropriate reduced differential algebraic equation (DAE) model with consistent initial values, which was tested with simple examples and a practical example. BioMed Central 2008-08-12 /pmc/articles/PMC2553091/ /pubmed/18694523 http://dx.doi.org/10.1186/1471-2105-9-338 Text en Copyright © 2008 Choi et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Choi, Junwon
Yang, Kyung-won
Lee, Tai-yong
Lee, Sang Yup
New time-scale criteria for model simplification of bio-reaction systems
title New time-scale criteria for model simplification of bio-reaction systems
title_full New time-scale criteria for model simplification of bio-reaction systems
title_fullStr New time-scale criteria for model simplification of bio-reaction systems
title_full_unstemmed New time-scale criteria for model simplification of bio-reaction systems
title_short New time-scale criteria for model simplification of bio-reaction systems
title_sort new time-scale criteria for model simplification of bio-reaction systems
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553091/
https://www.ncbi.nlm.nih.gov/pubmed/18694523
http://dx.doi.org/10.1186/1471-2105-9-338
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