genome-scale-metabolic-model

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

KEGG Module Evaluation Tool

GEMsembler tool for assembling and comparing several types of Genome-Scale Metabolic Models (GEMs)

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

The metabolic twin model of yeast

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

Python command-line software for whole-proteomes annotation based on structural homology.

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2024

Hands-on workshop for genome-scale metabolic model reconstruction using gapseq with Google Colab.

ECMproject is a standalone python program, which enumerates Elementary Conversion Modes (ECMs) of metabolic models.

Constraint-based metabolic modelling in your browser. 13 analyses over 4,659 strain GEMs and 12,340 growth media, solved client-side with glpk.js (WASM). Validated against COBRApy.

Species-agnostic pipeline that builds a pangenome-reference metabolic model and rapidly derives consistent, gap-filled strain-specific genome-scale models from bacterial genomes.

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models.

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Workflow for creation of Genome-Scale Metabolic Models and a Microbial Community Metabolic Model to model the human vaginal environment

Genome-scale metabolic model for engineering ABA production in Saccharomyces cerevisiae, derived from Yeast9 v9.1.0.

Supplementary material for "Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis"

GUI for GEMCAT Algorithm

Genome-scale metabolic model of Umbelopsis sp. WA50703

Analyse cellular metabolic states of cells from scRNA-seq data using FBA and Genome-scale Metabolic Models