The bacterial Model Reconstruction Service integrates and augments technologies for genome annotation, construction of gene-protein-reaction (GPR) associations, generation of biomass reactions, reaction network assembly, thermodynamic analysis of reaction reversibility, and model optimization, to generate draft genome-scale metabolic models. The service is capable of generating functioning draft metabolic models of an organism starting from an assembled genome sequence. Additional information is available in High-throughput generation, optimization and analysis of genome-scale metabolic models.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
This module provides the following application specfication(s):
- Orth, J.D., I. Thiele, and B.O. Palsson, What is flux balance analysis? Nat Biotechnol. 28(3): p. 245-8.
- Henry, C.S., et al., High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol, 2010. 28(9): p. 977-82.
- Overbeek, R., et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res, 2014. 42(Database issue): p. D206-14.
- Orth, J.D. and B.O. Palsson, Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng. 107(3): p. 403-12.