Biology subjects

Le Gregam, L.

Publications and source records attributed to Le Gregam, L..

2 recordsLinked to original sources

bioRxiv2024

MultiNMRFit: A software to fit 1D and pseudo-2D NMR spectra

Nuclear Magnetic Resonance (NMR) is widely used for quantitative analysis of metabolic systems. Accurate extraction of NMR signal parameters - such as chemical shift, intensity, coupling constants, and linewidth - is essential for obtaining information on the structure, concentration, and isotopic composition of metabolites. We present MultiNMRFit, an open-source software designed for high-throughput analysis of one-dimensional NMR spectra, whether acquired individually or as pseudo-2D experiments. MultiNMRFit extracts signal parameters (e.g. intensity, area, chemical shift, and coupling constants) by fitting the experimental spectra using built-in or user-defined signal models that account for multiplicity, providing high flexibility along with robust and reproducible results. The software is accessible both as a Python library and via a graphical user interface, enabling intuitive use by end-users with or without computational expertise. We demonstrate the robustness and flexibility of MultiNMRFit on 1H, 13C, and 31P NMR datasets collected in metabolomics and isotope labeling studies. Availability and ImplementationMultiNMRFit is implemented in Python 3 and was tested on Unix, Windows, and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/NMRTeamTBI/MultiNMRFit/. Supplementary dataSupplementary data are available online. ContactCyril Charlier (charlier@insa-toulouse.fr) and Pierre Millard (millard@insa-toulouse.fr)

bioinformatics↗

bioRxiv2023

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

SummaryQuantification 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 ImplementationPhysioFit is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. PhysioFit is also freely available online at https://workflow4metabolomics.org. The source code, the data and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/PhysioFit/ and https://physiofit.readthedocs.io/.

bioinformatics↗