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About MOST

Overview

• Sorting Tables
• Formula Bar
• Renaming Metabolites
• Renaming Compartments
• Visualization Overview

Installing MOST

• Requirements
• Windows
• Known Issues
• Linux
• Macintosh

File Menu

• Load SBML
• Load CSV
• Metabolites Column Selector
• Reactions Column Selector
• Add Metabolite Prompt
• Load Excel Spreadsheets
• Load from Model Collection
• Saving Files
• Save
• Save As SBML
• Save As CSV
• Clear Tables
• Exit

Analysis Menu

• FBA
• GDBB
• E-Flux2
• SPOT

Visualization Menu

• Visualize Compartment
• Show Visualization Report
• Locate Identifier Columns
• Set Edge Flux Levels
• Reset Edge Flux Levels to Default
• Visualization Frame Menus
• Save As SVG
• Save As PNG
• Find

Edit Menu

• Unused Metabolites
• Suspicious Metabolites
• Undo/Redo
• Find/Replace
• Select All
• Add Row/Column
• Unsort

Options Menu

• Select Solvers
• Set Solver Parameters
• Visualization Options
• Graph All in Database
• Scale Edge Thickness
• Ignore Water for Reaction Matching
• Show Visualization Report

Toolbar

• Save
• Copy/Paste
• Undo/Redo
• Find/Replace

Context Menus

• Table Menus
• Select Row(s)/Column(s)/Cell(s)
• Select All
• Copy/Paste
• Clear Contents
• Delete Row(s)
• Highlight Participating Reactions
• Un-Highlight Participating Reactions
• Reaction Editor
• Table Header Menus
• Delete Column
• Formula Bar Menu
• Console Menu
• Console Popout
• Tree Menu

Keyboard Shortcuts

• List of Keyboard Shortcuts

Visualization Options

Select Options –> Visualization Options -> (Alt+V then Alt+V) to view Visualization options.

A portion of a graph using the Graph All Reactions and Metabolites in Database option. Notice reactions not found in model are shown in subdued colors.

Graph All Reactions and Metabolites in Database:

Select Options –> Visualization Options -> Graph All Reactions and Metabolites in Database (Alt+O then Alt+V then Alt+G).

The default setting in for visualization is to graph the reactions found in the selected compartment of the loaded model. However, when building a model, it may be helpful to see all reactions in the database. Selection of this option will visualize all reactions in the database, and reactions not present in the model will be drawn using subdued colors.

A portion of a graph using default setting.

A portion of a graph using the "Graph All Reactions and Metabolites in Database" option. Notice reactions not found in model are shown in subdued colors.

Scale Edge Thickness Using Flux Values:

Select Options –> Visualization Options -> Scale Edge Thickness Using Flux Values (Alt+O then Alt+V then Alt+S).

The default setting in for visualization is to scale edge thicknesses using flux values. Deselecting this option will result in edges for all reactions found in the model to be the same thickness.

A portion of a graph with "Scale Edge Thickness Using Flux Values" unchecked.

Ignore Water for Reaction Matching:

Select Options –> Visualization Options -> Ignore Water for Reaction Matching (Alt+O then Alt+V then Alt+W).

Water is commonly omitted in reactions. Selecting the ignore water option will allow comparison with reactions in the database to be considered a match if water is not found in the reaction. For example a reaction A --> B + C will be graphed as reaction A + H2O --> B + C using this option.

Show Visualization Report:

Select Options –> Visualization Options -> Show Visualization Report (Alt+O then Alt+V then Alt+R).

The default setting in for visualization is to show a report listing reactions in three categories: reactions found in the model that are not present in the database, reactions where one or more metabolite does not have an identifier (KEGG id, ChEBI id, or Model SEED id), and reactions that have been graphed. Deselect this option to prevent this report from being shown when visualizing. The report can be viewed while visualizing by selecting Visualization --> Show Visualization Report (Alt+V then Alt+Z).