Genome-scale Metabolic Models

A genome-scale metabolic model (GSMM) is a specific microbial metabolic network composed of gene-protein (enzyme) – biochemical reaction associations by integrating genomics, transcriptomes, proteomics, and metabolomics data. GSMMs connect the biochemical reaction information obtained from the genome with the metabolic phenotype and provides an efficient platform for the systematic understanding of microbial physiological metabolic function models.

Applications

  • Prediction of Growth Phenotype
  • Guidance on Metabolic Engineering
  • Analysis of Evolutionary Differences between Species
  • Multi-omics Integration Analysis

GSMM Work Flow

genome-scale-metabolic-models

Database and Software

NumberDatabaseNumberSoftware
1Genbank1COBRA (Matlab)
2EMBL2Simpheny
3Ensembl3MetaFluxNet
4Uniprot4Pathway tools software
5MetaCyc5MosekSolver
6Pubchem6Cytoscape
7KEGG7Adobe Illustrator
8Pubmed8Cell Designer