genome-scale-metabolic-model 开源项目推荐（30 个）

franciscozorrilla /metaGEM

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

Matteopaluh /KEMET

KEGG模块评估工具

zimmermann-kogadeeva-group /GEMsembler

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

franciscozorrilla /EMBOMicroCom

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

LiLabTsinghua /Yeast-MetaTwin

The metabolic twin model of yeast

rcolpo /pgp_reconstruction

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

gioodm /wasp-proteins-annotation

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

franciscozorrilla /EMBOMicroCom2

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

kshitijtandon /fisabio-gapseq-workshop

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

c-mayer /ECMproject

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

mahjalili /ssGSEAGEM

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

robbedewin /PaRMMoSaHN

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

draeger-lab /C_striatum_GEMs

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

C-CoMP-STC /MIT1002-GEM

A manually-curated metabolic model for Alteromonas macleodii MIT1002

natJimenez /eukaryo_methods

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

CASB-NAU /yeast-aba-gem

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

V-Varga /Vaginomics__GEMs_MCMM

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

mdziurzynski /iUmbe1-GEM

Genome-scale metabolic model of Umbelopsis sp. WA50703

MolecularBioinformatics /gemcat_gui

GUI for GEMCAT Algorithm

omicspilot /CellMetPro

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