MOST - Metabolic Optimization and Simulation Tool

Note: Results of Analyses are not editable. After running an Analysis, the result will be selected in the tree (panel on right side of MOST). When a result is selected, any menu item that could be used to change the results will be grayed out. This includes most of the menu items in the Edit menu and Context menus.

Table Menus:

Each table cell has a context (right-click menu). They all contain “Select All”, “Copy”, “Paste”, “Clear Contents”, and “Delete Row(s)”. The Reactions table also has a “Un-Highlight Participating Reactions” menu item. There are some columns that contain additional entries such as “Launch Reaction Editor” in the Reaction Equation (Metabolite Abbreviation) column, and “Rename”, “Highlight Participating Reactions”, and “Un-Highlight Participating Reactions” in the Metabolite Abbreviation and Metabolite Name columns.

Select Row(s)/Column(s)/Cell(s):

Select has three sub-menu items, which allows table selection modes to be changed between selecting entire rows, columns, or individual cells. The default setting is individual cells.

Select All:

Select All has two sub-menu items with radio buttons: “Include Column Names” and “Select Table Cells Only” so that the table contents can be copied into an external program such as Microsoft Excel with or without the column names. Ctrl+A selects all cells but does not include column names.

Copy/Paste:

Copy can also be executed with Clrl+C or using the Copy icon on the Toolbar.

Paste can also be executed with Clrl+V or using the Paste icon on the Toolbar. Paste will be grayed out on columns that are not editable and in optimization results tables.

Clear Contents:

Clear Contents can also be executed with Clrl+E. Clear Contents will be grayed out on columns that are not editable and in optimization results tables.

Delete Row(s):

Rows in the metabolites table cannot be deleted if they contain “used” metabolites – that is metabolites that participate in one or more reactions. See Unused Metabolites.

Highlight Participating Reactions:

Highlight Participating Reactions will tab to the Reactions table, and scroll the first participating reaction of the selected metabolite into view. If the metabolite is unused, this menu item will be grayed out. If the selected cell is changed in the metabolites table, the reactions will be un-highlighted.

Un-Highlight Participating Reactions:

Un-Highlight Participating Reactions in either table will un-highlight reactions.

Reaction Editor:

Launch Reaction Editor will launch the Reaction Editor. If the selected row is changed in the Reactions table, the Reaction Editor will close.

Please note that to commit an entry and update Reaction Equation when editing a Reactant or Product drop box, the Enter or Tab keys must be pressed, or field selection must be changed to another active cell.

Table Header Menus:

Delete Column:

Column Headers have a context menu with “Delete Column”, but columns can only be deleted if they are not core columns, so this menu item will be grayed out on core columns.

Formula Bar Menu:

The Formula Bar has "Cut", "Copy", "Paste", "Delete" and "Select All" menu items.

Console Menu:

The console (lower pane) is where the output information is displayed after running analyses. The context menu of the console can be used to view MPS (Mathematical Programming System) files for analyses if the "Save to MPS File" option was selected in the Set Solver Parameters dialogs. The context menu also contains “Copy”and “Select All. “Pop Out” will open the Console Popout that will display the contents of the console and allow the user to save results of analyses as text (.txt) files. The Console and Popout both have "Copy" and "Select All" menu items. The Console Popout can also be used to open text files.

Console Popout:

Tree Menu:

The top item in the tree panel (right pane) is the model name, and does not have a context menu. When Analyses are run, new items are added to the tree. All of these items have context menus which contain the items "Delete" which deletes the currently selected optimization, and "Delete All Optimizations"