opencobra / COBRA.tutorials

Related projects ⓘ

Alternatives and complementary repositories for COBRA.tutorials

• SBRG / cobrame
  A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
  ☆34Updated 5 years ago
• mmundy42 / mackinac
  Mackinac: A bridge between ModelSEED and COBRApy
  ☆16Updated 6 years ago
• ginkgobioworks / geckopy
  Enzyme-constrained genome-scale models in python
  ☆25Updated last year
• ModelSEED / ModelSEEDDatabase
  This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…
  ☆56Updated 3 weeks ago
• opencobra / m_model_collection
  A collection of M models downloaded from published studies
  ☆15Updated 8 years ago
• jclachance / BOFdat
  Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
  ☆26Updated last year
• cdanielmachado / reframed
  ReFramed: metabolic modeling package
  ☆56Updated 2 months ago
• jdbrunner / surfin_fba
  Dynamic FBA for use with COBRApy metabolic models
  ☆10Updated last year
• draeger-lab / ModelPolisher
  ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
  ☆23Updated last week
• klamt-lab / straindesign
  StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
  ☆39Updated last month
• SBRG / bigg_models
  The BiGG Models website server
  ☆80Updated 5 years ago
• segrelab / comets
  Computation of Microbial Ecosystems in Time and Space
  ☆19Updated this week
• ThieleLab / CodeBase
  Code depository for papers
  ☆20Updated last week
• cnapy-org / CNApy
  An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced feat…
  ☆46Updated last month
• MetabolicAtlas / standard-GEM
  The standard for open-source GEMs on GitHub
  ☆19Updated last year
• cdanielmachado / framed
  framed: a metabolic modeling package for python
  ☆25Updated 5 years ago
• SystemsBioinformatics / cbmpy
  CBMPy is a Python based platform for constraint based modelling and analysis.
  ☆19Updated 5 months ago
• latendre / PythonCyc
  ☆22Updated 4 years ago
• SBRG / cobradb
  COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is a…
  ☆20Updated 5 years ago
• pstjohn / d3flux
  D3.js based visualizations of cobrapy metabolic models
  ☆41Updated 4 years ago
• RamanLab / metquest
  Enumerating biosynthetic pathways in metabolic networks
  ☆12Updated last year
• SysBioChalmers / RAVEN
  The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
  ☆101Updated last week
• ModelSEED / ModelSEEDpy
  Python package for building and analyzing models using ModelSEED
  ☆18Updated this week
• Toepfer-Lab / cobramod
  CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway inf…
  ☆12Updated 3 months ago
• SysBioChalmers / GECKO
  Toolbox for including enzyme constraints on a genome-scale model.
  ☆67Updated 3 weeks ago
• borenstein-lab / CoMiDA
  The code and distributable for designing minimal microbial communities with specified metabolic functions.
  ☆11Updated 7 years ago
• VirtualMetabolicHuman / AGORA
  The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gu…
  ☆20Updated 3 years ago
• jrjhealey / bioinfo-tools
  Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
  ☆55Updated 4 years ago
• micom-dev / micom
  Python package to study microbial communities using metabolic modeling.
  ☆94Updated last week
• opencobra / memote
  memote – the genome-scale metabolic model test suite
  ☆128Updated 10 months ago