Finding minimal generating set for metabolic network with reversible pathways

Dimitrije Jevremović; Daniel Boley

doi:10.1016/j.biosystems.2013.02.003

Finding minimal generating set for metabolic network with reversible pathways

Dimitrije Jevremović, Daniel Boley

Computer Science and Engineering

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Elementary flux modes give a mathematical representation of metabolic pathways in metabolic networks satisfying the constraint of non-decomposability. The large cost of their computation shifts attention to computing a minimal generating set which is a conically independent subset of elementary flux modes. When a metabolic network has reversible reactions and also admits a reversible pathway, the minimal generating set is not unique. A theoretical development and computational framework is provided which outline how to compute the minimal generating set in this case. The method is based on combining existing software to compute the minimal generating set for a " pointed cone" together with standard software to compute the Reduced Row Echelon Form.

Original language	English (US)
Pages (from-to)	31-36
Number of pages	6
Journal	BioSystems
Volume	112
Issue number	1
DOIs	https://doi.org/10.1016/j.biosystems.2013.02.003
State	Published - Apr 2013

Bibliographical note

Funding Information:
We would like to acknowledge the support by NSF grant 0916750, IBM Ph.D. fellowship program and Biomedical Informatics and Computational Biology Program of the University of Minnesota, Rochester.

Keywords

Elementary flux modes
Metabolic networks
Metabolic pathways
Minimal generating set

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10.1016/j.biosystems.2013.02.003

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abstract = "Elementary flux modes give a mathematical representation of metabolic pathways in metabolic networks satisfying the constraint of non-decomposability. The large cost of their computation shifts attention to computing a minimal generating set which is a conically independent subset of elementary flux modes. When a metabolic network has reversible reactions and also admits a reversible pathway, the minimal generating set is not unique. A theoretical development and computational framework is provided which outline how to compute the minimal generating set in this case. The method is based on combining existing software to compute the minimal generating set for a {"} pointed cone{"} together with standard software to compute the Reduced Row Echelon Form.",

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T1 - Finding minimal generating set for metabolic network with reversible pathways

AU - Jevremović, Dimitrije

AU - Boley, Daniel

N1 - Funding Information: We would like to acknowledge the support by NSF grant 0916750, IBM Ph.D. fellowship program and Biomedical Informatics and Computational Biology Program of the University of Minnesota, Rochester.

PY - 2013/4

Y1 - 2013/4

N2 - Elementary flux modes give a mathematical representation of metabolic pathways in metabolic networks satisfying the constraint of non-decomposability. The large cost of their computation shifts attention to computing a minimal generating set which is a conically independent subset of elementary flux modes. When a metabolic network has reversible reactions and also admits a reversible pathway, the minimal generating set is not unique. A theoretical development and computational framework is provided which outline how to compute the minimal generating set in this case. The method is based on combining existing software to compute the minimal generating set for a " pointed cone" together with standard software to compute the Reduced Row Echelon Form.

AB - Elementary flux modes give a mathematical representation of metabolic pathways in metabolic networks satisfying the constraint of non-decomposability. The large cost of their computation shifts attention to computing a minimal generating set which is a conically independent subset of elementary flux modes. When a metabolic network has reversible reactions and also admits a reversible pathway, the minimal generating set is not unique. A theoretical development and computational framework is provided which outline how to compute the minimal generating set in this case. The method is based on combining existing software to compute the minimal generating set for a " pointed cone" together with standard software to compute the Reduced Row Echelon Form.

KW - Elementary flux modes

KW - Metabolic networks

KW - Metabolic pathways

KW - Minimal generating set

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Finding minimal generating set for metabolic network with reversible pathways

Abstract

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Keywords

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