COBRApy is a package for constraint-based modeling of metabolic networks.
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
💎 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.
The consensus GEM for Saccharomyces cerevisiae
Python package to study microbial communities using metabolic modeling.
SMETANA: a tool to analyse interactions in microbial communities
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!
Infer metabolic directions from moment differences of mass-weighted intensity distributions
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Curation and analysis of metabolic models
KEGG Module Evaluation Tool
Materials and presentation for the 2022 ISB Microbiome course.
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Materials and presentation for the 2023 ISB Microbiome course.
Open source genome-scale metabolic models of human and model animals
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