Repositories list

• AKR1A1-Deficiency-in-Cancer-Metabolic-Modeling

  Public
  Genome-scale metabolic modeling workflow investigating AKR1A1 deficiency as a metabolic vulnerability in renal cell carcinoma and hepatocellular carcinoma. Inte…

  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 14, 2026Jul 14, 2026

• rFastcormics4cobra_09062026

  Public
  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  MATLAB

  •

  Other

  •336336 forks•00 stars•00 issues•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• rFASTCORMICS

  Public
  papermetabolic-networks

  papermetabolic-networks

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •11 fork•77 stars•11 issue•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• SLFN11_figure

  Public
  short script for figure in SLFN11 review paper

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 16, 2026Jun 16, 2026

• Valceschini_et_al_2025

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 22, 2026May 22, 2026

• WILDkCAT

  Public
  Extract, Retrieve and Predict kcat values for a metabolic model

  apienzymemetabolic-models+ 5

  apienzymemetabolic-modelsmetabolic-reconstructionbrendakcatturnover-numbersabio-rk

  HTML

  •

  MIT License

  •00 forks•88 stars•11 issue•00 pull requests•Updated May 12, 2026May 12, 2026

• ISB705MetabolicNetworkModeling

  Public
  teachingmetabolic-networks

  teachingmetabolic-networks

  HTML

  •11 fork•11 star•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• MetabolicMediaLibrary

  Public
  A repository dedicated to standardizing culture media definitions for genome-scale metabolic modeling.

  Julia

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• Clinical_Biomarker_Detection

  Public
  DRIVEN-DTU WP13: Biomarker Detection In Clinical Cohort Data Using Machine Learning

  machine-learningpaper

  machine-learningpaper

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• PD-rSNP_SCARB2

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• scFASTCORMICS

  Public
  papermetabolic-networks

  papermetabolic-networks

  MATLAB

  •11 fork•00 stars•11 issue•00 pull requests•Updated Oct 28, 2025Oct 28, 2025

• cancer_epigenetics_FUSO

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 11, 2025Jul 11, 2025

• Multi-tissue-model

  Public
  papermetabolic-networks

  papermetabolic-networks

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jul 3, 2025Jul 3, 2025

• RasCilium

  Public
  paper

  paper

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2025Jun 2, 2025

• pypglm_main

  Public
  Temporary repo for Master thesis evaluation

  signaling-networks

  signaling-networks

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 13, 2025Jan 13, 2025

• FALCON

  Public
  FALCON: A Toolbox for the Fast Contextualization of Logical Networks

  papersignaling-networks

  papersignaling-networks

  MATLAB

  •

  GNU General Public License v3.0

  •55 forks•77 stars•00 issues•00 pull requests•Updated Jan 10, 2025Jan 10, 2025

• GliomaGEM

  Public
  Glioma metabolic modelling for repurposing of single and combination drugs

  papermetabolic-networks

  papermetabolic-networks

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 30, 2024Nov 30, 2024

• MidbrainOrganoid_Miro1_scMetabMod

  Public
  Multi-cell population modelling predicts metabolic activity of midbrain organoids

  metabolic-networks

  metabolic-networks

  MATLAB

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 27, 2024Nov 27, 2024

• Helgueta_et_al_2023

  Public
  Companion repo for the article by Sergio Helgueta et al.

  paper

  paper

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 5, 2024Nov 5, 2024

• DeepOncoAI

  Public
  ML cancer drug sensitivity

  machine-learning

  machine-learning

  Python

  •11 fork•33 stars•00 issues•00 pull requests•Updated Nov 4, 2024Nov 4, 2024

• IHEC_metabolism

  Public
  papermetabolic-networks

  papermetabolic-networks

  11 fork•11 star•00 issues•00 pull requests•Updated Jul 26, 2024Jul 26, 2024

• cobratoolbox_rFASTCORMICS

  Public
  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  metabolic-networks

  metabolic-networks

  MATLAB

  •

  Other

  •336336 forks•00 stars•00 issues•00 pull requests•Updated Jun 29, 2024Jun 29, 2024

• AKR1A1-Deficiency

  Public
  metabolic-networks

  metabolic-networks

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2024Apr 30, 2024

• MedicagoScripts

  Public
  MATLAB

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 2, 2024Apr 2, 2024

• IDARE

  Public
  IDARE - Multiomics Visualisation in Cytoscape

  papercytoscapemetabolic-networks

  papercytoscapemetabolic-networks

  Java

  •

  GNU Lesser General Public License v3.0

  •11 fork•22 stars•00 issues•22 pull requests•Updated Dec 5, 2023Dec 5, 2023

• NutriHuMiX

  Public
  papermetabolic-networks

  papermetabolic-networks

  00 forks•00 stars•00 issues•00 pull requests•Updated Nov 7, 2023Nov 7, 2023

• MelanomaPaper

  Public
  Consensus models of Bintener et al. 2023

  papermetabolic-networks

  papermetabolic-networks

  00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2023Jul 21, 2023

• cobratoolbox

  Public
  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  MATLAB

  •

  Other

  •336336 forks•00 stars•00 issues•00 pull requests•Updated Jul 7, 2023Jul 7, 2023

• GomezRamos_et_al_2023

  Public
  paper

  paper

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 2, 2022Nov 2, 2022

• IDARE-QuickStart

  Public
  metabolic-networks

  metabolic-networks

  00 forks•11 star•00 issues•00 pull requests•Updated Jun 27, 2022Jun 27, 2022