openCOBRA

Repositories

• memote

  memote – the genome-scale metabolic model test suite

  unit-testing standardization cobra metabolic-models sbml metabolic-reconstruction
  HTML Apache-2.0 17 65 98 1 Updated Jun 17, 2020

• MASSef
  Mathematica 2 0 16 (2 issues need help) 0 Updated Jun 16, 2020

• cobratoolbox

  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  tutorial metabolomics reconstruction transcriptomics cobra metabolic-models strain-engineering
  MATLAB GPL-3.0 218 142 33 (1 issue needs help) 3 Updated Jun 12, 2020

• COBRA.jl

  High-level, high-performance, constraint-based reconstruction and analysis in Julia

  analysis high-performance julia cobra large-scale high-level constraint-based-modeling
  Julia GPL-3.0 26 40 6 (1 issue needs help) 4 Updated Jun 12, 2020

• cobrapy

  COBRApy is a package for constraint-based modeling of biological networks

  python flux bioinformatics modeling systems-biology computational-biology biochemistry
  Python GPL-2.0 163 242 63 (5 issues need help) 12 Updated Jun 11, 2020

• cobra-component-models

  Provide SQLAlchemy ORM and pydantic data models for SQL storage and serialization of COBRA components such as reactions, compounds, and compartments.

  serialization sqlalchemy orm cobra pydantic
  Python Apache-2.0 0 0 0 0 Updated Apr 25, 2020

• cobrapy-website
  HTML LGPL-3.0 4 0 0 1 Updated Apr 10, 2020

• COBRA.tutorials

  Repository of tutorials for The COBRA Toolbox

  tutorials reconstruction systemsbiology cobra metabolic-models constraint-based-modeling cobratoolbox
  MATLAB 21 11 5 0 Updated Apr 7, 2020

• COBRA.models

  Set of models used for testing COBRA code in continuous integration environments
  Julia 1 0 0 1 Updated Apr 7, 2020

• Medusa

  Analysis of ensembles of metabolic network reconstructions
  Python MIT 5 12 26 8 Updated Mar 31, 2020

• cookiecutter-python-package

  Extensive cookiecutter template for openCOBRA Python packages.
  Python Apache-2.0 0 0 0 0 Updated Mar 6, 2020

• COBRA.papers

  Repository for scripts related to reproducing the results of an individual publication
  MATLAB 5 4 1 1 Updated Feb 27, 2020

• memote-docker

  Easily use the memote command line interface from a docker container.

  docker-container cobra sbml sbml-model memote memote-command
  Shell Apache-2.0 1 2 0 1 Updated Dec 7, 2019

• kb_memote

  Forked from janakagithub/kb_memote
  Python MIT 2 1 0 0 Updated Dec 3, 2019

• driven

  Data-Driven Constraint-based analysis
  Python Apache-2.0 11 9 4 3 Updated Aug 15, 2019

• cookiecutter-memote

  A cookiecuttter template for memote model repositories
  Python MIT 2 2 3 0 Updated Apr 10, 2019

• artenolis

  Automated Reproducibility and Testing Environment for Licensed Software

  automation continuous-integration computational-biology test-driven-development software-quality cobra artenolis
  3 2 0 0 Updated Apr 2, 2019

• MATLAB.devTools

  MATLAB Development Tools
  MATLAB GPL-3.0 22 26 1 0 Updated Mar 29, 2019

• COBRA.java

  Constraint-based reconstruction and analysis via Java
  0 0 0 0 Updated Mar 28, 2019

• opencobra.github.io

  Official openCOBRA website
  CSS MIT 3 0 0 0 Updated Mar 1, 2019

• memote-webservice Archived

  Run memote in a microservice with a frontend that allows you to upload and test models.
  Python Apache-2.0 4 0 1 0 Updated Jan 7, 2019

• COBRA.binary

  Linux, Windows and Mac binaries maintained by the constraint-based reconstruction and analysis community
  MATLAB 5 2 1 0 Updated Jul 31, 2018

• cobrapy-bigg-client
  Python Apache-2.0 0 1 0 0 Updated Jun 6, 2018

• schema

  xml/rdf schemas for annotating cobra models
  Apache-2.0 1 2 10 0 Updated Sep 6, 2017

• MASS-Toolbox

  Mass Action Stoichiometric Simulation (MASS) Toolbox
  Mathematica 7 10 20 1 Updated Aug 1, 2017

• m_model_collection

  A collection of M models downloaded from published studies
  Jupyter Notebook 15 12 2 0 Updated Feb 18, 2016

• pypi_cobrapy_travis

  hosts binary wheel installers for unit testing
  C 0 0 0 0 Updated Nov 11, 2015

• cobrapy_shim

  Shim for the COBRA toolbox to call cobrapy functions
  Python 0 1 0 0 Updated Sep 9, 2015