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37 search results found

Cobrapy ⭐ 414

COBRApy is a package for constraint-based modeling of metabolic networks.

Cobratoolbox ⭐ 232

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

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

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

memote – the genome-scale metabolic model test suite

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

Yeast Gem ⭐ 80

The consensus GEM for Saccharomyces cerevisiae

Python package to study microbial communities using metabolic modeling.

Metage2metabo ⭐ 42

From annotated genomes to metabolic screening in large scale microbiotas

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!

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Curation and analysis of metabolic models

Isb_course_2022 ⭐ 22

Materials and presentation for the 2022 ISB Microbiome course.

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

Metabolicatlas ⭐ 18

Open source genome-scale metabolic models of human and model animals

Cobra.tutorials ⭐ 18

Repository of tutorials for The COBRA Toolbox

KEGG Module Evaluation Tool

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

Fluctuator ⭐ 13

R package to Import and Modify SVG (XML) Graphic Files

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.

Pgp_reconstruction ⭐ 10

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Isb_course_2023 ⭐ 10

Materials and presentation for the 2023 ISB Microbiome course.

Misosoup ⭐ 10

Minimal Supplying Community Search with constraint-based optimization methods.

Q2 Micom ⭐ 10

A Qiime plugin for MICOM.

SMETANA: a tool to analyse interactions in microbial communities

Autopacmen ⭐ 10

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

Pygenprop ⭐ 9

A python library for programmatic usage of EBI InterPro Genome Properties.

A Universal Modeling Language for Metabolic Flux Analysis

Advancesyntoolkit ⭐ 7

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Reconstruct and handle many genome-scale metabolic models in ScrumPy

Yarrowia_lipolytica_w29 Gem ⭐ 5

Genome-scale model of Yarrowia lipolytica.

Environmental growth media for MICOM.

Microberx ⭐ 5

Cnapy Projects ⭐ 5

🗺️ A repository of CNApy projects

Physiofit ⭐ 5

Estimation of extracellular fluxes and growth rate

Memote M Capsulatus ⭐ 5

Genome-scale metabolic model of Methylococcus capsulatus.

Dynamically load balanced FVA through a hybrid MPI/OpenMP architecture.

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