F2C2
- Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/.
Author details: | Abdelhalim Larhlimi, Laszlo DavidGND, Joachim SelbigGND, Alexander BockmayrORCiD |
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URN: | urn:nbn:de:kobv:517-opus4-432431 |
DOI: | https://doi.org/10.25932/publishup-43243 |
ISSN: | 1866-8372 |
Title of parent work (German): | Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe |
Subtitle (English): | a fast tool for the computation of flux coupling in genome-scale metabolic networks |
Publication series (Volume number): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (921) |
Publication type: | Postprint |
Language: | English |
Date of first publication: | 2020/05/28 |
Publication year: | 2012 |
Publishing institution: | Universität Potsdam |
Release date: | 2020/05/28 |
Tag: | balance analysis; couple reaction; coupling relationship; linear programming problem; metabolic network; models; pathways; reconstruction; reversible reaction |
Issue: | 921 |
Number of pages: | 11 |
Source: | BMC Bioinformatics 13 (2012) 57 DOI: 10.1186/1471-2105-13-57 |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät |
DDC classification: | 0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik |
5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie | |
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit | |
Peer review: | Referiert |
Publishing method: | Open Access |
License (German): | Keine öffentliche Lizenz: Unter Urheberrechtsschutz |
External remark: | Bibliographieeintrag der Originalveröffentlichung/Quelle |