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The Top 23 Metabolic Models Open Source Projects

Open source projects categorized as Metabolic Models
Categories > Metabolic Models
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101most recent commit 7 months agopypi cobra} Downloads
Cobratoolbox ⭐ 232
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
most recent commit 5 months ago
Metagem ⭐ 155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
most recent commit 5 months ago
Gapseq ⭐ 131
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
most recent commit 5 months ago
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61most recent commit 5 months agopypi memote} Downloads
Raven ⭐ 87
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
most recent commit 7 months ago
Yeast Gem ⭐ 80
The consensus GEM for Saccharomyces cerevisiae
most recent commit 6 months ago
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101most recent commit 5 months agopypi micom} Downloads
Metage2metabo ⭐ 42
From annotated genomes to metabolic screening in large scale microbiotas
total releases 33most recent commit 5 months ago
Cnapy ⭐ 36
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
most recent commit 5 months ago
Cobrame ⭐ 29
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
most recent commit 5 years ago
Psamm ⭐ 26
Curation and analysis of metabolic models
dependent packages 2total releases 32most recent commit 2 years agopypi psamm} Downloads
Isb_course_2022 ⭐ 22
Materials and presentation for the 2022 ISB Microbiome course.
most recent commit 8 months ago
Corda ⭐ 20
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
total releases 14most recent commit 6 months ago
Metabolicatlas ⭐ 18
Open source genome-scale metabolic models of human and model animals
most recent commit a year ago
Cobra.tutorials ⭐ 18
Repository of tutorials for The COBRA Toolbox
most recent commit 5 months ago
Kemet ⭐ 15
KEGG Module Evaluation Tool
most recent commit 7 months ago
Bofdat ⭐ 14
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
total releases 7most recent commit 5 years ago
Fluctuator ⭐ 13
R package to Import and Modify SVG (XML) Graphic Files
most recent commit a year ago
Agora ⭐ 11
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
most recent commit 4 years ago
Pgp_reconstruction ⭐ 10
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
most recent commit 7 months ago
Isb_course_2023 ⭐ 10
Materials and presentation for the 2023 ISB Microbiome course.
most recent commit 8 months ago
Misosoup ⭐ 10
Minimal Supplying Community Search with constraint-based optimization methods.
total releases 13most recent commit 7 months ago
The 4 Most Depended On Metabolic Models Open Source Projects
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101latest release October 31, 2023most recent commit 7 months agopypi cobra} Downloads
Psamm ⭐ 26
Curation and analysis of metabolic models
dependent packages 2total releases 32latest release May 22, 2015most recent commit 2 years agopypi psamm} Downloads
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61latest release November 21, 2023most recent commit 5 months agopypi memote} Downloads
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101latest release October 29, 2023most recent commit 5 months agopypi micom} Downloads
The 10 Latest Releases In Metabolic Models Open Source Projects
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61latest release November 21, 2023most recent commit 5 months agopypi memote} Downloads
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101latest release October 31, 2023most recent commit 7 months agopypi cobra} Downloads
Micom ⭐ 73
Python package to study microbial communities using metabolic modeling.
dependent packages 1total releases 101latest release October 29, 2023most recent commit 5 months agopypi micom} Downloads
Metage2metabo ⭐ 42
From annotated genomes to metabolic screening in large scale microbiotas
total releases 33latest release September 26, 2022most recent commit 5 months ago
Misosoup ⭐ 10
Minimal Supplying Community Search with constraint-based optimization methods.
total releases 13latest release August 18, 2022most recent commit 7 months ago
Pygenprop ⭐ 9
A python library for programmatic usage of EBI InterPro Genome Properties.
total releases 5latest release January 19, 2022most recent commit a year ago
Q2 Micom ⭐ 10
A Qiime plugin for MICOM.
total releases 13latest release October 08, 2021most recent commit 5 months ago
Smetana ⭐ 10
SMETANA: a tool to analyse interactions in microbial communities
total releases 5latest release October 16, 2019most recent commit 4 years ago
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