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Model Reconstruction Service

Overview

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 service is no longer supported on the BV-BRC website.

About this module

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):

See also

References

  1. Orth, J.D., I. Thiele, and B.O. Palsson, What is flux balance analysis? Nat Biotechnol. 28(3): p. 245-8.
  2. Henry, C.S., et al., High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol, 2010. 28(9): p. 977-82.
  3. 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.
  4. Orth, J.D. and B.O. Palsson, Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng. 107(3): p. 403-12.