Using ModelView - Part 2: Viewing Model Details

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This is part of the tutorial series Using ModelView.

General Info

After you have selected a model, you can use the tools within the Model SEED to examine the information for that model. The tools organize the data associated with the model into maps and tables that make it easy for the user to search or browse for relevant information.

Upon selecting the model, you are greeted with an overview page. This contains information about the organism and the model. You can download the complete model in differnet formats (SBML, Model SEED, and LP), and deselect this model from this page as well.

General Model Info

Underneath the first set of tabs is another tabbed interface which contains the model information.


Maps Tab

One way the data is organized is by KEGG pathways. The model information is overlaid onto the KEGG maps with a color scheme to determine the state of the compounds and reactions.

To see a list of all the available maps, click the "Map Select" bar.

Map Select

Clicking on one of the links causes the new map to show up in place of the current map.

A legend tells the user how to interpret the colors. The compounds (circles) can have the following attributes: Transported, Represented, or Biomass. If the compound is gray, then it is not in the model. The reactions (rectangle) are colored according to the organism that is currently selected. If a reaction appears purple, then it is gapfilled.

Annotated KEGG Map

Reaction Tab

Reaction Tab

To view all the reactions in the model, click on the 'Reactions' tab. This brings up a table containing each reaction and some general information. The table contains the following columns:

Reaction Table Header

This table can be searched and sorted via the column headers. Also, you can hide columns by clicking on the '...' in the last column and unselecting column names.

Reaction Table Header Select

Here is an overview of the links inside the reaction table.

Reaction Table Details

Compound Tab

Compound Tab

To view all the compounds in the model, click on the 'Compounds' tab. This tab contains a table with additional information about each compound.

Compound Table

Gene Tab

Gene Tab

Selecting the 'Gene' tab brings up a table containing all the genes in the model. This table shows information about the gene, such as the peg annotation, the functional assignment, and the essentiality.

Gene Table

Clicking on one of the peg links opens a new page devoted to that peg annotation in the currently selected organism. For example, the below image was for 'peg.100' in the table above. This is just a sample of some of the information shown on this page.

Annotation Example

Continue on to Part 3: Comparing Two or More Models

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About this Entry

This page contains a single entry by The SEED Team published on August 18, 2010 3:31 PM.

Using ModelView - Part 3: Comparing Two or More Models was the previous entry in this blog.

Using ModelView - Part 5: Running Flux-Balance Analysis on Models is the next entry in this blog.

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