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@tibbdc Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

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    33 repositories

    • ECMpy-document

      Public
      User Manual for ECMpy
      Python
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • SEEK

      Public
      A human in the loop framework for building high quality biological databases using Large Language Models
      Apache License 2.0
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • ermer

      Public
      Python
      •
      Apache License 2.0
      •2•4•0•0•Updated Aug 29, 2025Aug 29, 2025

    • ecBSU1

      Public
      Construction and application of the genome-scale enzyme‐constrained model of Bacillus subtilis
      Jupyter Notebook
      •
      Other
      •1•2•0•0•Updated Aug 29, 2025Aug 29, 2025

    • aaomics

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • DeepSub

      Public
      DeepSub is a tool designed to predict the number of subunits in a protein sequence for homo-oligomers.
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Aug 29, 2025Aug 29, 2025

    • MTD

      Public
      Code related to constructing the MTD database.
      HTML
      •
      Other
      •0•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • modulome_cgluta

      Public
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • ecCGL1

      Public
      Construction and application of the Corynebacterium glutamicum enzyme‐constrained model
      Jupyter Notebook
      •
      Other
      •1•2•0•0•Updated Aug 29, 2025Aug 29, 2025

    • ETGEMs

      Public
      Jupyter Notebook
      •
      Other
      •3•10•1•0•Updated Aug 29, 2025Aug 29, 2025

    • ECMpy

      Public template
      Jupyter Notebook
      •
      Other
      •4•18•1•1•Updated Aug 29, 2025Aug 29, 2025

    • GO-HKP

      Public
      A Gene Ontology Hierarchy-Driven Framework for Enzyme kcat Prediction
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Aug 29, 2025Aug 29, 2025

    • MTLKP

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • PEAR

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • eciZM547

      Public
      The enzyme-constrained model of Zymomonas mobilis
      Jupyter Notebook
      •1•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • RSSP-AutoML

      Public
      regulatory sequences strength prediction based on AutoML
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Apr 23, 2024Apr 23, 2024

    • ecMTM

      Public
      Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
      Jupyter Notebook
      •1•0•0•0•Updated Apr 23, 2024Apr 23, 2024

    • Tpho

      Public
      Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis
      Python
      •1•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • AutoESDCas

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jan 30, 2024Jan 30, 2024

    • psa-GEM

      Public
      The genome-scale metabolic model of Pseudomonas stutzeri A1501
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • ECRECer

      Public
      Dual-core Multi-agent Learning Framework For EC Number Prediction
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Apr 18, 2023Apr 18, 2023

    • AutoESD

      Public
      Python
      •1•3•0•0•Updated Apr 21, 2022Apr 21, 2022

    • scp4ssd

      Public
      Python
      •0•0•1•0•Updated Apr 16, 2022Apr 16, 2022

    • GEDpm-cg

      Public
      Python
      •0•0•0•0•Updated Aug 31, 2021Aug 31, 2021

    • GraphCM

      Public
      A new method for the processing of currency metabolites in metabolic networks based on graph theory
      Jupyter Notebook
      •3•3•0•0•Updated Jul 5, 2021Jul 5, 2021

    • bow-tie

      Public
      bow tie structure analysis
      Python
      •1•1•0•0•Updated Dec 14, 2020Dec 14, 2020

    • cookiecutter-reproducible-science

      Public
      boilerplate for reproducible and transparent science
      Other
      •94•1•0•0•Updated Sep 16, 2020Sep 16, 2020

    • vna-GEM

      Public template
      genome scale metabolic model for Vibrio natriegens
      standard-gem
      standard-gem
      Creative Commons Attribution 4.0 International
      •1•1•0•0•Updated Sep 7, 2020Sep 7, 2020

    • ECMpy-old

      Public
      ECMpy
      Jupyter Notebook
      •0•1•0•0•Updated Aug 31, 2020Aug 31, 2020

    • cobrapy

      Public
      COBRApy is a package for constraint-based modeling of metabolic networks.
      Python
      •
      GNU General Public License v2.0
      •234•0•0•0•Updated Aug 16, 2020Aug 16, 2020
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