Repositories list

• met4j

  Public
  Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses …

  Java

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• dexom-python

  Public
  diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

  pythonoptimizationmetabolism+ 3

  pythonoptimizationmetabolismcobrapyconstraint-based-modelingomics-data-integration

  Python

  •

  GNU General Public License v3.0

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

• metexplore3api_client_r

  Public
  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 2, 2025Sep 2, 2025

• insilico_metabolic_analyses_tutorials_and_courses

  Public
  In this repo are listed all the public resources to learn in silico metabolic analyses

  11 fork•11 star•00 issues•11 pull request•Updated Sep 1, 2025Sep 1, 2025

• miom

  Public
  Constraint-based modeling of metabolism using Mixed Integer Optimization

  pythonoptimizationmodeling+ 7

  pythonoptimizationmodelingmilpmetabolismreconstructioncobrapyflux-balance-analysisconstraint-based-modelinggenome-scale

  Python

  •

  GNU General Public License v3.0

  •22 forks•1212 stars•88 issues•00 pull requests•Updated Sep 24, 2024Sep 24, 2024

• MetExploreViz

  Public
  JavaScript

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 13, 2022Oct 13, 2022

• metexplore2_maintenance

  Public
  HTML

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jun 23, 2022Jun 23, 2022

• dexom

  Public
  Diversity-based enumeration of optimal context-specific metabolic networks

  optimizationmetabolismmetabolic-network+ 6

  optimizationmetabolismmetabolic-networkmetabolic-reconstructionconstraint-based-modelingmetabolic-engineeringcobra-toolboxomics-data-integrationmetabolic-pathways

  MATLAB

  •

  GNU General Public License v3.0

  •11 fork•77 stars•22 issues•00 pull requests•Updated Jul 2, 2021Jul 2, 2021

• dexom-evaluation

  Public
  DEXOM submodule with data for evaluation

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 18, 2020Nov 18, 2020

• cobratoolbox-lib

  Public
  COBRA Toolbox without submodules and minor modifications to improve reproducibility

  MATLAB

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2020Jul 21, 2020

• phnmnl-FingerprintClustering

  Public
  Performs unsupervised clustering among a metabolic network from a fingerprint

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 26, 2018Jul 26, 2018

• phnmnl-PathwayEnrichment

  Public
  pathway enrichment tool for Docker containerization into Galaxy PhenoMeNal instance

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 26, 2018Jul 26, 2018

• container-computeDistanceMatrix

  Public
  Shell

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 15, 2018Jun 15, 2018

• computeDistanceMatrix

  Public
  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2018Jun 15, 2018

• container-PathwayEnrichment

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 16, 2017Nov 16, 2017

• tool-SBML2MetexploreJsonGraph

  Public archive
  Java

  •

  GNU Lesser General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 28, 2017Jun 28, 2017

• MetaboliteIDConverter

  Public archive
  Java

  •

  GNU Lesser General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 19, 2017Jun 19, 2017

• tool-PathwayEnrichment

  Public archive
  Java

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2017Apr 24, 2017