Model Reconstruction Service¶
The 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.
Using the Model Reconstruction Service¶
The Model Reconstruction submenu option under the Services main menu (Metabolomics category) opens the Reconstruct Metabolic Model input form (shown below). Note: You must be logged into PATRIC to use this service. The Model Reconstruction service is also available via the PATRIC Command Line Interface (CLI).
Model Reconstruction Menu
Model Reconstruction Input Form
Select a Genome¶
Select a public genome or a genome from workspace
Note: click the filter icon to the left of the genome input box to help in finding your genomes
Selection for a predefined media formulation from a dropdown list for this model to be gapfilled and simulated for flux-balance analysis (FBA), e.g., GMM – Glucose Minimal Media, NMS- Nitrate Mineral Salts Medium, LB - Luria-Bertani Medium.
The workspace folder where results will be placed.
Name used to uniquely identify results.