multiTFA: a Python package for multi-variate thermodynamics-based flux analysis.
| Autor: | Mahamkali V; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia., McCubbin T; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia., Beber ME; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark., Noor E; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel., Marcellin E; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia., Nielsen LK; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. |
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| Jazyk: | angličtina |
| Zdroj: | Bioinformatics (Oxford, England) [Bioinformatics] 2021 Sep 29; Vol. 37 (18), pp. 3064-3066. |
| DOI: | 10.1093/bioinformatics/btab151 |
| Abstrakt: | Motivation: We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation of the group contribution methodology. Overall, the method greatly reduces the uncertainty of thermodynamic variables. Results: We present multiTFA, a Python implementation of our framework. We evaluated our application using the core Escherichia coli model and achieved a median reduction of 6.8 kJ/mol in reaction Gibbs free energy ranges, while three out of 12 reactions in glycolysis changed from reversible to irreversible. Availability and Implementation: Our framework along with documentation is available on https://github.com/biosustain/multitfa. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2021. Published by Oxford University Press.) |
| Databáze: | MEDLINE |
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