Skip to content

Tutorial 4: Importing from model SEED

Jump to bottom
John May edited this page May 8, 2013 · 8 revisions

This page will guide you through the steps to import a model from model-SEED. Once the model is imported it can be annotated using the same tools described in Tutorial 1. Before you start, as with the first tutorial there are several resources which should be loaded - Resources.

Downloading your model

When logged into to model-SEED, navigate to the 'User models' tab of model-SEED and select Excel format from the available download links.

download-model

Create a reconstruction

Before importing the model we need to create a reconstruction. To create a new reconstruction the menu item File>New Reconstruction is used. A dialog will be displayed that allows for input of organism information.

New Reconstruction

Input the organism information for your model, please refere to Creating a reconstruction for a detailed explanation each field.

Importing the file into Metingear

There are two ways to import this file into Metingear. The menu item File > Import model-SEED (xls) will require only that you select the file. The other option is File > Import Excel which is more flexible but requires extensive configuration. The Import model-SEED item actually just provides a preset config specific for the layout of the model-SEED worksheets. Importing Microsoft Excel Worksheets provides more information about the configuration. Due to the unstructured nature of the input this setup can be difficult and for this tutorial we will use the preconfigured File > Import model-SEED (xls).

file-import

With the menu item selected, choose the location of the file you downloaded earlier.

file-select

After a short wait the reactions and metabolites will have been imported into the active reconstruction.

import-complete

Below is a summary of how column name in the model-SEED spreadsheet relates to the entities in Metingear.

  • Metabolites (Compounds sheet)
    • DATABASE is loaded as metabolite abbreviation
    • PRIMARY NAME is loaded metabolite name
    • KEGG ID(S) are loaded cross-references to KEGG Compound
    • FORMULA and CHARGE are loaded as formula and charge annotations
  • Reactions
    • DATABASE is loaded as reaction abbreviation
    • NAME is loaded reaction name
    • EC Number is loaded as an Enzyme Nomenclature cross-reference
    • DELTA G and DELTA G ERROR are loaded as Gibbs energy annotations
    • DIRECTION defines the direction of the reactions
    • EQUATION is used to build the participants of the reactions

With the data imported you can proceed to annotate and modify the model using the tools described in the first tutorial.

Clone this wiki locally