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22 repositories

PhysioFit
Public
Estimation of extracellular fluxes and growth rate
synthetic-biology systems-biology metabolism
synthetic-biology systems-biology metabolism mass-spectrometry biotechnology metabolic-models nuclear-magnetic-resonance fluxomics metabolic-flux-analysis isotope-labeling-experiments
Python
•
GNU General Public License v3.0
•5•9•1•0•Updated Nov 30, 2025Nov 30, 2025
DynafluxR_notebook
Public
Showcase DynafluxR.
dynamical-systems metabolomics fluxomics
dynamical-systems metabolomics fluxomics metabolic-flux-analysis
HTML
•
GNU General Public License v3.0
•0•1•0•0•Updated Aug 22, 2025Aug 22, 2025
dynafluxr
Public
Calculate Flux Dynamics from Dynamic Concentrations of Metabolites
modeling systems-biology metabolomics
modeling systems-biology metabolomics mass-spectrometry nuclear-magnetic-resonance fluxomics metabolic-flux-analysis
R
•0•1•0•0•Updated Jul 7, 2025Jul 7, 2025
glucose_acetate_bioproduction
Public
Exploiting acetate for glucose-based bioproduction in E. coli
HTML
•
GNU General Public License v3.0
•0•1•0•0•Updated Jun 23, 2025Jun 23, 2025
IsoDesign
Public
IsoDesign is a scientific tool to design 13C-fluxomics experiments.
Python
•
GNU General Public License v3.0
•2•0•0•0•Updated Jun 17, 2025Jun 17, 2025
IsoCor
Public
IsoCor: Isotope Correction for mass spectrometry labeling experiments
metabolomics mass-spectrometry ms-data
metabolomics mass-spectrometry ms-data isotope fluxomics metabolic-flux-analysis 13c-mfa isotope-labeling-experiments isotope-correction correction-natural-abundance
Python
•
GNU General Public License v3.0
•9•24•6•0•Updated Apr 25, 2025Apr 25, 2025
in_vivo_enzymatic_parameters
Public
In vivo analysis of enzymatic parameters
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 25, 2024Jul 25, 2024
Peiro_2019
Public
Supplementary code of Peiro et al., 2019
R
•
GNU General Public License v3.0
•0•0•0•0•Updated May 29, 2024May 29, 2024
ethanolamine_metabolism
Public
Ethanolamine metabolism of E. coli
Component Pascal
•
GNU General Public License v3.0
•0•0•0•0•Updated Mar 1, 2024Mar 1, 2024
GL_GNT_bypass
Public
13C metabolic flux analysis of the extracellular GL-GNT by-pass of E. coli
systems-biology metabolism escherichia-coli
systems-biology metabolism escherichia-coli dynamic-model 13c-mfa 13c-fluxomics gluconolactone gluconate pentose-phosphate-pathway
Component Pascal
•
GNU General Public License v3.0
•0•1•0•0•Updated Nov 27, 2023Nov 27, 2023
pseudomonas_metabolic_burden
Public
Flux response of Pseudomonas putida to increased levels of metabolic burden
biotechnology metabolic-models fluxomics
biotechnology metabolic-models fluxomics 13c-mfa protein-production pseudomonas-putida metabolic-burden
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 26, 2023Jul 26, 2023
glucose_acetate_interplay
Public
Supplementary information of Millard et al. 2023
flux systems-biology regulation
flux systems-biology regulation predictive-modeling glucose biotechnology escherichia-coli copasi kinetic-modeling metabolic-control
HTML
•
GNU General Public License v3.0
•1•0•0•0•Updated Jun 20, 2023Jun 20, 2023
PhysioFit4Galaxy
Public
Maintainance of the Physiofit package for the W4M Galaxy instance
Python
•
GNU General Public License v3.0
•5•0•0•0•Updated Nov 14, 2022Nov 14, 2022
acetate_regulation
Public
Kinetic modeling of glucose and acetate metabolisms in E. coli
systems-biology regulation dynamical-systems
systems-biology regulation dynamical-systems metabolism metabolomics dynamical-modeling escherichia-coli metabolic-models metabolic-network copasi
Component Pascal
•
GNU General Public License v3.0
•2•7•0•0•Updated Mar 17, 2021Mar 17, 2021
IsoSolve_notebook
Public
Showcase IsoSolve
systems-biology nmr metabolomics
systems-biology nmr metabolomics mass-spectrometry emu fluxomics isotopomer cumomer isotopologue isotope-labeling-experiments
HTML
•
GNU Affero General Public License v3.0
•2•3•0•0•Updated Mar 15, 2021Mar 15, 2021
IsoSolve
Public
Integration of isotopic measurements
systems-biology nmr metabolomics
systems-biology nmr metabolomics ms fluxomics isotopomer cumomer isotopologue isotope-labeling-experiments elementary-metabolite-unit
Python
•
Other
•2•4•0•0•Updated Mar 8, 2021Mar 8, 2021
zerter
Public
Extract signals from J-resolved NMR spectra (Cox et al., 2020)
nmr metabolomics nmr-spectroscopy
nmr metabolomics nmr-spectroscopy jres
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Sep 30, 2020Sep 30, 2020
IsoQ
Public
Simultaneous measurement of absolute metabolite concentration and isotope incorporation by mass spectrometry
metabolomics mass-spectrometry ms-data
metabolomics mass-spectrometry ms-data isotope fluxomics metabolic-flux-analysis 13c-mfa isotope-labeling-experiments isotopologue-distribution
Python
•
GNU General Public License v3.0
•1•2•0•0•Updated Dec 13, 2019Dec 13, 2019
IsoSim
Public
IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems
synthetic-biology systems-biology dynamical-systems
synthetic-biology systems-biology dynamical-systems metabolic-models kinetic-modeling metabolic-flux-analysis 13c-mfa stoichiometric-modeling 13c-fluxomics
R
•
GNU General Public License v3.0
•4•6•1•0•Updated Sep 12, 2019Sep 12, 2019
FindPath
Public
FindPath
MATLAB
•0•0•0•0•Updated Jul 8, 2019Jul 8, 2019
Interact
Public
Analysis of 1D and 2D NMR titration experiments.
nmr protein-protein-interaction protein-ligand-interactions
nmr protein-protein-interaction protein-ligand-interactions titration nmr-data
Python
•
GNU General Public License v3.0
•1•1•0•0•Updated Jun 12, 2019Jun 12, 2019
KinetX
Public
Supplementary code of Cox et al., 2019
metabolism nmr-data enzyme-kinetics
metabolism nmr-data enzyme-kinetics in-vitro-enzymology
Python
•1•0•0•0•Updated Nov 13, 2018Nov 13, 2018

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MetaSys team (Toulouse Biotechnology Institute)

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All

22 repositories

PhysioFit

DynafluxR_notebook

dynafluxr

glucose_acetate_bioproduction

IsoDesign

IsoCor

in_vivo_enzymatic_parameters

Peiro_2019

ethanolamine_metabolism

GL_GNT_bypass

pseudomonas_metabolic_burden

glucose_acetate_interplay

PhysioFit4Galaxy

acetate_regulation

IsoSolve_notebook

IsoSolve

zerter

IsoQ

IsoSim

FindPath

Interact

KinetX

All

All

Repositories list

22 repositories