Repositories list

• dexom-python

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

  optimizationmetabolismcobrapy+ 3constraint-based-modelingomics-data-integrationpython

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 21, 2024Nov 21, 2024

• 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 relevant to metabolism-related research.

  Java

  •0•1•0•0•Updated Oct 31, 2024Oct 31, 2024

• miom

  Public
  Constraint-based modeling of metabolism using Mixed Integer Optimization

  modelingmilpmetabolism+ 7reconstructioncobrapyflux-balance-analysisconstraint-based-modelinggenome-scalepythonoptimization

  Python

  •

  GNU General Public License v3.0

  •2•11•8•0•Updated Sep 24, 2024Sep 24, 2024

• MetExploreViz

  Public
  JavaScript

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 13, 2022Oct 13, 2022

• metexplore2_maintenance

  Public
  HTML

  •0•0•2•0•Updated Jun 23, 2022Jun 23, 2022

• dexom

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

  optimizationmetabolismmetabolic-network+ 6metabolic-reconstructionconstraint-based-modelingmetabolic-engineeringomics-data-integrationmetabolic-pathwayscobra-toolbox

  MATLAB

  •

  GNU General Public License v3.0

  •1•5•2•0•Updated Jul 2, 2021Jul 2, 2021

• dexom-evaluation

  Public
  DEXOM submodule with data for evaluation

  Jupyter Notebook

  •0•0•0•0•Updated Nov 18, 2020Nov 18, 2020

• cobratoolbox-lib

  Public
  COBRA Toolbox without submodules and minor modifications to improve reproducibility

  MATLAB

  •

  Other

  •0•0•0•0•Updated Jul 21, 2020Jul 21, 2020

• phnmnl-FingerprintClustering

  Public
  Performs unsupervised clustering among a metabolic network from a fingerprint

  R

  •0•1•0•0•Updated Jul 26, 2018Jul 26, 2018

• phnmnl-PathwayEnrichment

  Public
  pathway enrichment tool for Docker containerization into Galaxy PhenoMeNal instance

  Java

  •0•0•0•0•Updated Jul 26, 2018Jul 26, 2018

• container-computeDistanceMatrix

  Public
  Shell

  •1•0•0•0•Updated Jun 15, 2018Jun 15, 2018

• computeDistanceMatrix

  Public
  Java

  •0•0•0•0•Updated Jun 15, 2018Jun 15, 2018

• container-PathwayEnrichment

  Public
  Shell

  •0•0•0•0•Updated Nov 16, 2017Nov 16, 2017

• tool-SBML2MetexploreJsonGraph

  Public archive
  Java

  •

  GNU Lesser General Public License v3.0

  •1•0•0•0•Updated Jun 28, 2017Jun 28, 2017

• MetaboliteIDConverter

  Public archive
  Java

  •

  GNU Lesser General Public License v3.0

  •2•0•0•0•Updated Jun 19, 2017Jun 19, 2017

• tool-PathwayEnrichment

  Public archive
  Java

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Apr 24, 2017Apr 24, 2017