Repositories list

• ECMpy

  Public template
  Jupyter Notebook

  •

  MIT License

  •4•13•0•1•Updated Mar 20, 2025Mar 20, 2025

• Metabolic-network-model

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• PEAR

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• MTD

  Public
  Code related to constructing the MTD database.

  HTML

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• mcCGL1

  Public
  The first multi-constrained GEMs for Corynebacterium glutamicum

  Jupyter Notebook

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• 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

• DeepSub

  Public
  DeepSub is a tool designed to predict the number of subunits in a protein sequence for homo-oligomers.

  Jupyter Notebook

  •0•1•0•0•Updated Mar 28, 2024Mar 28, 2024

• ECMpy-document

  Public
  User Manual for ECMpy

  Python

  •0•0•0•0•Updated Mar 14, 2024Mar 14, 2024

• AutoESDCas

  Public
  Jupyter Notebook

  •0•2•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

• ETGEMs

  Public
  Jupyter Notebook

  •3•9•1•0•Updated Aug 1, 2023Aug 1, 2023

• ECRECer

  Public
  Dual-core Multi-agent Learning Framework For EC Number Prediction

  Jupyter Notebook

  •

  MIT License

  •3•0•0•0•Updated Apr 18, 2023Apr 18, 2023

• aaomics

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 24, 2023Mar 24, 2023

• ecBSU1

  Public
  Construction and application of the genome-scale enzyme‐constrained model of Bacillus subtilis

  Jupyter Notebook

  •1•1•0•0•Updated Jan 5, 2023Jan 5, 2023

• ecCGL1

  Public
  Construction and application of the Corynebacterium glutamicum enzyme‐constrained model

  Jupyter Notebook

  •1•2•0•0•Updated Jan 5, 2023Jan 5, 2023

• AutoESD

  Public
  Python

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

• scp4ssd

  Public
  Python

  •0•0•0•0•Updated Apr 16, 2022Apr 16, 2022

• ermer

  Public
  Python

  •

  Apache License 2.0

  •2•4•0•0•Updated Mar 29, 2022Mar 29, 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•0•0•0•Updated Dec 14, 2020Dec 14, 2020

• cookiecutter-reproducible-science

  Public
  boilerplate for reproducible and transparent science

  Other

  •78•1•0•0•Updated Sep 16, 2020Sep 16, 2020

• vna-GEM

  Public template
  genome scale metabolic model for Vibrio natriegens

  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

  •220•0•0•0•Updated Aug 16, 2020Aug 16, 2020

• standard-GEM

  Public template
  The standard for open-source GEMs on GitHub

  Creative Commons Attribution 4.0 International

  •5•0•0•0•Updated Jul 15, 2020Jul 15, 2020

• tibbdc.github.io

  Public
  www.ibiodesign.net

  HTML

  •0•0•0•0•Updated May 18, 2020May 18, 2020