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    32 repositories

    • ecETFL

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • SubNetX

      Public
      Python
      •
      MIT License
      •0•3•1•0•Updated Jul 16, 2025Jul 16, 2025

    • pytfa

      Public
      A Python 3 implementation of Thermodynamics-based Flux Analysis
      Linear Programming
      •
      Apache License 2.0
      •29•39•10•2•Updated Jul 9, 2025Jul 9, 2025

    • etfl

      Public
      ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
      Python
      •
      Apache License 2.0
      •19•16•3•3•Updated Jul 8, 2025Jul 8, 2025

    • NICEgame

      Public
      Linear Programming
      •
      Apache License 2.0
      •5•5•0•0•Updated Jun 23, 2025Jun 23, 2025

    • skimpy

      Public
      Symbolic Kinetic Models with Python
      Python
      •
      Apache License 2.0
      •15•32•2•0•Updated Jun 4, 2025Jun 4, 2025

    • NOMAD

      Public
      A Python implementation of the NOMAD workflow for rational strain design using large-scale kinetic models.
      Python
      •3•1•0•0•Updated May 19, 2025May 19, 2025

    • LaTeX

      Public
      Scripts and instructions for the paper titled: ''Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration"
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • yetfl

      Public
      Python
      •
      Apache License 2.0
      •4•4•4•0•Updated Mar 31, 2025Mar 31, 2025

    • iNTS_SL1344

      Public
      Genome-scale metabolic model of Salmonella Typhimurium SL1344.
      MATLAB
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • matTFA

      Public
      A Matlab implementation of Thermodynamics-based Flux Analysis
      HTML
      •
      GNU General Public License v3.0
      •12•3•3•0•Updated Oct 15, 2024Oct 15, 2024

    • host_parasite_interactions

      Public
      Generating host-parasite metabolic models to investigate the dependence of the parasite on the host's metabolic genes
      Objective-C
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 11, 2024Jun 11, 2024

    • redgem

      Public
      MATLAB
      •
      Apache License 2.0
      •2•2•0•0•Updated May 30, 2024May 30, 2024

    • remind

      Public
      Python
      •
      Apache License 2.0
      •0•4•0•0•Updated Mar 19, 2024Mar 19, 2024

    • RENAISSANCE

      Public
      REconstruction of dyNAmIc models through Stratified Sampling using Artificial Neural networks and Concepts of Evolution strategies
      Apache License 2.0
      •3•15•1•1•Updated Mar 1, 2024Mar 1, 2024

    • open

      Public
      OPtimal ENzyme - Estimates catalytically optimal modes of operations of enzymatic reactions
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Apr 14, 2023Apr 14, 2023

    • BridgITplus

      Public
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Jan 30, 2023Jan 30, 2023

    • rekindle

      Public
      REKINDLE is a python package for training the generative adversarial networks (GANs) to parametrize large-scale nonlinear kinetic models of cellular metabolism
      Python
      •
      Apache License 2.0
      •4•9•1•0•Updated Oct 11, 2022Oct 11, 2022

    • ARBRE

      Public
      Python
      •1•3•0•0•Updated May 18, 2022May 18, 2022

    • ATLASxAnalyses

      Public
      The data and scripts contained in this repository allow the user to reproduce the figures and analyses of the article "ATLASx: a computational map for the exploration of biochemical space", doi: https://doi.org/10.1101/2021.02.17.431583
      Python
      •
      Apache License 2.0
      •0•4•0•0•Updated Jan 31, 2022Jan 31, 2022

    • matMCP

      Public
      MATLAB
      •0•0•0•0•Updated Sep 8, 2021Sep 8, 2021

    • cromics

      Public
      CROMICS: CROwding-Modeling of In-silico Community Systems
      MATLAB
      •
      Apache License 2.0
      •0•2•0•0•Updated Jun 22, 2021Jun 22, 2021

    • nicepath

      Public
      Python
      •1•4•0•0•Updated Mar 8, 2021Mar 8, 2021

    • NRA

      Public
      Constraint-based metabolic control analysis for rational strain engineering
      MATLAB
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 4, 2021Feb 4, 2021

    • phenomapping

      Public
      PhenoMapping is a computational framework that provides some workflows and methodologies for the understanding of mechanisms underlying phenotypes using genome-scale models (GEMs). PhenoMapping classifies the information in a GEM as organism-specific information and context-specific information. Organism-specific information includes the (i) bio…
      MATLAB
      •
      Apache License 2.0
      •2•2•0•0•Updated Nov 14, 2020Nov 14, 2020

    • redhuman

      Public
      redHUMAN: analyzing human metabolism and growth media through systematic reductions of thermodynamically curated genome-scale models
      MATLAB
      •
      Apache License 2.0
      •1•5•0•0•Updated Aug 31, 2020Aug 31, 2020

    • texfba

      Public
      Integration of gene expression data with TFA constraints
      MATLAB
      •
      Apache License 2.0
      •2•2•0•0•Updated Nov 14, 2019Nov 14, 2019

    • ci_ensemble_modeling

      Public
      MATLAB
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 10, 2019Oct 10, 2019

    • remi

      Public
      Relative Expression and Metabolite Integration
      MATLAB
      •2•4•2•0•Updated Apr 15, 2019Apr 15, 2019

    • geek

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Apr 15, 2019Apr 15, 2019