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    34 repositories

    • 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 Feb 26, 2026Feb 26, 2026

    • RENAISSANCE

      Public
      REconstruction of dyNAmIc models through Stratified Sampling using Artificial Neural networks and Concepts of Evolution strategies
      Jupyter Notebook
      •
      Apache License 2.0
      •3•18•1•0•Updated Feb 13, 2026Feb 13, 2026

    • SubNetX

      Public
      Python
      •
      MIT License
      •0•6•1•0•Updated Dec 1, 2025Dec 1, 2025

    • remind

      Public
      Reconstructing metabolic interaction networks in microbial communities using genome-scale metabolic models
      Python
      •
      Apache License 2.0
      •1•6•0•0•Updated Nov 19, 2025Nov 19, 2025

    • human-cancer-kinetic-models

      Public
      Multi-omics–informed large-scale kinetic models capturing cancer metabolism, drug response, and BRCA1-associated metabolic rewiring.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • nis

      Public
      MATLAB
      •
      Apache License 2.0
      •0•1•0•0•Updated Oct 16, 2025Oct 16, 2025

    • ecETFL

      Public
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Jul 21, 2025Jul 21, 2025

    • pytfa

      Public
      A Python 3 implementation of Thermodynamics-based Flux Analysis
      Linear Programming
      •
      Apache License 2.0
      •29•45•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
      •17•17•3•3•Updated Jul 8, 2025Jul 8, 2025

    • NICEgame

      Public
      Linear Programming
      •
      Apache License 2.0
      •4•5•0•0•Updated Jun 23, 2025Jun 23, 2025

    • skimpy

      Public
      Symbolic Kinetic Models with Python
      Python
      •
      Apache License 2.0
      •14•35•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•2•1•0•Updated May 19, 2025May 19, 2025

    • yetfl

      Public
      Python
      •
      Apache License 2.0
      •4•5•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
      •13•5•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
      •2•0•1•0•Updated Jun 11, 2024Jun 11, 2024

    • redgem

      Public
      MATLAB
      •
      Apache License 2.0
      •2•3•0•0•Updated May 30, 2024May 30, 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
      •3•10•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 explo…
      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-…
      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
      •2•6•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
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