Rocha, Isabel | Search NASA

DOE OSTI2020

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

MEMOTE for standardized genome-scale metabolic model testing

Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organism’s metabolism under different conditions. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Gene–protein–reaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with metadata can be built using standard reconstruction protocols, and guidelines have been put in place for tracking provenance and enabling interoperability, but a standardized means of quality control for GEMs is lacking. Here we report a community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality.

59 BASIC BIOLOGICAL SCIENCES↗