PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.

Autor:	Le Grégam L; Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France.; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France., Guitton Y; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.; Oniris, INRAE, LABERCA, Nantes, 44307, France., Bellvert F; Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France.; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France., Heux S; Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France., Jourdan F; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.; Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, 31027, France., Portais JC; Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France.; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.; RESTORE (Geroscience & Rejuvenation Center), Université de Toulouse, INSERM, CNRS, EFS, Toulouse, 31100, France., Millard P; Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France.; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Aug 02; Vol. 40 (8).
DOI:	10.1093/bioinformatics/btae488
Abstrakt:	Summary: Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and extracellular substrates and products. A single tool is available to non-computational biologists to calculate extracellular fluxes, but it is hardly interoperable and is limited to a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any growth model and is interoperable by design. PhysioFit includes some of the most common growth models, and advanced users can implement additional models to calculate extracellular fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative kinetics. PhysioFit can be used as a Python library and offers a graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines. Availability and Implementation: PhysioFit v3 is implemented in Python 3 and was tested on Windows, Unix, and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/PhysioFit/ and https://physiofit.readthedocs.io/. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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