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
Python package to study microbial communities using metabolic modeling.
The consensus GEM for Saccharomyces cerevisiae
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
From annotated genomes to metabolic screening in large scale microbiotas
SMETANA: a tool to analyse interactions in microbial communities
An integrated visual environment for metabolic modeling 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
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
R package to Import and Modify SVG (XML) Graphic Files
Open source genome-scale metabolic models of human and model animals
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
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