Repositories list

• k-sacce306

  Public
  K-FIT kinetic models for Saccharomyces cerevisiae CEN.PK and BY4741

  MATLAB

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• CatPred

  Public
  Machine Learning models for in vitro enzyme kinetic parameter prediction

  deep-learningmlregression+ 4

  deep-learningmlregressionpython3pytorchenzyme-kineticsprotein-property-prediction

  Python

  •

  MIT License

  •2929 forks•9595 stars•55 issues•11 pull request•Updated Jun 15, 2026Jun 15, 2026

• auxotroph-design

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• yeastsMFA

  Public
  Repository for yeasts MFA related files

  metabolismmetabolic-flux-analysis

  metabolismmetabolic-flux-analysis

  MATLAB

  •22 forks•33 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• MechFind

  Public
  Jupyter Notebook

  •00 forks•77 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• KETCHUP

  Public
  Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP)

  Python

  •11 fork•55 stars•11 issue•00 pull requests•Updated Jan 12, 2026Jan 12, 2026

• scRBA

  Public
  S. cerevisiae Resource Balance Analysis model

  metabolismflux-balance-analysisconstraint-based-modeling+ 1

  metabolismflux-balance-analysisconstraint-based-modelingresource-balance-analysis

  GAMS

  •

  MIT License

  •44 forks•22 stars•00 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• rtRBA

  Public
  Resource Balance Analysis model for Rhodotorula toruloides IFO0880

  HTML

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• I_orientalis_organic_acids

  Public
  Simulations of _Issatchenkia orientalis_ producing organic acids

  11 fork•00 stars•00 issues•00 pull requests•Updated Nov 10, 2025Nov 10, 2025

• chemo-enz

  Public
  Expanding chemical synthesis planning to explore chemo-enzymatic pathways using minimal transitions

  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 14, 2025Aug 14, 2025

• iPavir

  Public
  Genome-scale metabolic model of Panicum virgatum

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• ctRBA

  Public
  Repository for genome-scale resource balance analysis model of Clostridium thermocellum, ctRBA

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2025May 14, 2025

• novoStoic2.0

  Public
  novoStoic2.0: Integrated Pathway Design Tool with Thermodynamic Considerations and Enzyme Selection

  Jupyter Notebook

  •99 forks•1111 stars•00 issues•00 pull requests•Updated Apr 28, 2025Apr 28, 2025

• Protein-InDelMaker

  Public
  A Rosetta-based Python tool for constructing user-defined variant libraries with amino acid insertions, deletions, using loop closure algorithms and energy mini…

  numpyprotein-structurepython3+ 1

  numpyprotein-structurepython3pyrosetta

  Python

  •11 fork•33 stars•00 issues•00 pull requests•Updated Jan 17, 2025Jan 17, 2025

• optstoic-gams

  Public
  optStoic-minFlux/minRxn code for PMID: 26530953

  GAMS

  •

  Apache License 2.0

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 25, 2024Apr 25, 2024

• CatPred-DB

  Public
  Python

  •

  MIT License

  •22 forks•55 stars•11 issue•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• iSace_GSM

  Public
  Repository of a genome-scale metabolic model for Saccharomyces cerevisiae

  metabolismyeastconstraint-based-modeling+ 2

  metabolismyeastconstraint-based-modelingmetabolic-modelsaccharomyces-cerevisiae

  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 11, 2024Mar 11, 2024

• iPotri3463

  Public
  This repository contains multi-tissue metabolic models of populus trichocarpa

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 15, 2024Feb 15, 2024

• dGPredictor

  Public
  Jupyter Notebook

  •33 forks•1010 stars•11 issue•11 pull request•Updated Dec 15, 2023Dec 15, 2023

• iCTH669

  Public
  Repository for the Stoichiometric Genome-Scale Model (GSM) of Clostridium thermocellum

  HTML

  •00 forks•44 stars•00 issues•00 pull requests•Updated Oct 11, 2023Oct 11, 2023

• CNN_seq_CoV2

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 28, 2023Sep 28, 2023

• EnzRank

  Public
  PureBasic

  •22 forks•55 stars•00 issues•00 pull requests•Updated May 18, 2023May 18, 2023

• iRhto_memote

  Public
  Memote-created repository for Rhodosporidium toruloides model iRhto

  metabolismyeastconstraint-based-modeling+ 1

  metabolismyeastconstraint-based-modelingmetabolic-model

  HTML

  •

  Creative Commons Attribution 4.0 International

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 1, 2023Mar 1, 2023

• kcat-km

  Public
  Predictive models for estimating kcat and km of enzymes from sequence/structure information

  Python

  •22 forks•33 stars•00 issues•00 pull requests•Updated Nov 14, 2022Nov 14, 2022

• SNPeffect

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 24, 2022Feb 24, 2022

• k-ctherm138

  Public
  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 7, 2022Feb 7, 2022

• ensembledocking

  Public
  Codes for ensemble docking

  00 forks•00 stars•00 issues•00 pull requests•Updated Jan 10, 2022Jan 10, 2022

• SteadyState-MFA

  Public
  Genome scale steady state 13C metabolic flux analysis

  MATLAB

  •44 forks•44 stars•22 issues•00 pull requests•Updated Nov 30, 2021Nov 30, 2021

• uncFBA

  Public
  metabolismuncertainty-propagationflux-balance-analysis+ 1

  metabolismuncertainty-propagationflux-balance-analysisconstraint-based-modeling

  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated Nov 2, 2021Nov 2, 2021

• dGPredictor-py2

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•22 stars•22 issues•11 pull request•Updated Aug 9, 2021Aug 9, 2021