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    13 repositories

    • Gemma4EC

      Public
      Gemma4EC: reaction classification LLM.
      synthetic-biologyenzymesllms
      synthetic-biologyenzymesllms
      Python
      •0•0•0•0•Updated May 28, 2026May 28, 2026

    • ECNumberPrediction

      Public
      EC Number prediction methods
      deep-learningreactionsfingerprinting
      deep-learningreactionsfingerprintingenzymes
      Python
      •0•0•0•0•Updated May 4, 2026May 4, 2026

    • cyclic-gMISpy

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 29, 2026Apr 29, 2026

    • gMCSpy

      Public
      Efficient calculation of gMCS in python.
      metabolismgmcspygenetic-minimal-cut-sets
      metabolismgmcspygenetic-minimal-cut-setsgmcs
      Python
      •
      MIT License
      •1•6•1•0•Updated Dec 17, 2025Dec 17, 2025

    • iMR_gMIS_paper_scripts

      Public
      Scripts to generate all the results of the paper of iMR gmis calculation
      MATLAB
      •0•1•0•0•Updated May 6, 2025May 6, 2025

    • q2-metnet

      Public
      QIIME 2 plugin to contextualize taxonomic abundance data into high-quality metabolic reconstruction of the human gut microbiota
      Python
      •4•3•1•0•Updated Feb 3, 2025Feb 3, 2025

    • gmctool

      Public
      A tool for discovering metabolic vulnerabilities in cancer research
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • BN-BacArena

      Public
      Bayesian Network implementation of BacArena
      MATLAB
      •0•4•0•0•Updated Mar 11, 2024Mar 11, 2024

    • gmcs_meta_analysis

      Public
      Scripts to generate all the results and the figures in the paper of gmctool meta-analysis
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • AGREDA

      Public
      AGREDA (AGORA-based REconstruction for Diet Analysis) is a new repository of genome-scale metabolic models of human gut microbes.
      MATLAB
      •2•0•0•0•Updated Nov 1, 2023Nov 1, 2023

    • iMR_gmcs

      Public
      Scripts to generate all the results and the figures in the paper of iMR gmcs calculation
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated May 19, 2023May 19, 2023

    • iMR_gmcs_paper_scripts

      Public
      Scripts to generate all the results and the figures in the paper of iMR gmcs calculation
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated May 19, 2023May 19, 2023

    • AGREDA_1.1

      Public
      Python
      •2•1•0•0•Updated Apr 27, 2023Apr 27, 2023
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