Model Reconstruction Service

Overview

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

Options

Model Reconstruction Input Form

Select a Genome

Select a public genome or a genome from workspace

Genome

Note: click the filter icon to the left of the genome input box to help in finding your genomes

Optional Parameters

Media

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.

Output Folder

The workspace folder where results will be placed.

Output Name

Name used to uniquely identify results.

Buttons

Reset: Resets the input form to default values

Reconstruct: Launches the model reconstruction job.