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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

Solver Parameters

Gurobi Parameters

Select Options –> Set Gurobi Parameters (Alt+O then Alt+G).

The Set Gurobi Parameters dialog will appear:

Gurobi Parameters Descriptions:

Feasibility Tolerance – Primal feasibility tolerance.

Integer Feasibility Tolerance – Integer feasibility tolerance. Only affects mixed integer programming (MIP) models.

Dual Feasibility Tolerance – Optimality tolerance.

Heuristics – Turn mixed integer programming (MIP) heuristics up or down. Only affects MIP models

MIP Focus – Set the focus of the mixed integer programming (MIP) solver. Only affects MIP models

Number of Threads – Number of parallel threads to use.

Save to MPS File - MOST can write a mixed integer programming (MIP) problem to an MPS (Mathematical Programming System) file if true is selected. The MPS file can be accessed from the Console Menu "View MPS File" menu item.

The Gurobi Reference Manual contains descriptions of Gurobi solver parameters.

GNU Linear Programming Kit (GLPK) Parameters

Select Options –> Set GLPK Parameters (Alt+O then Alt+L).

The Set GLPK Parameters dialog will appear:

The GNU Linear Programming Kit Reference Manual contains descriptions of GLPK solver parameters.

Feasibility Tolerance, Integer Feasibility Tolerance - see GLPK Reference Manual pg. 67.

MIP gap - also known as the duality gap (GLPK Reference Manual pg. 126).

Save to MPS File - MOST can write a mixed integer programming (MIP) problem to an MPS (Mathematical Programming System) file if true is selected - see GLPK Reference Manual, Appendix B. The MPS file can be accessed from the Console Menu "View MPS File" menu item.

Ipopt Parameters

Select Options –> Set Ipopt Parameters (Alt+O then Alt+l).

The Set Ipopt Parameters dialog will appear:

Descriptions of Ipopt parameters can be found here.

Ipopt will detect and choose HSL or Pardiso solvers as default if they are placed in the "MOST" installation directory lib/win32, lib/win64, lib/linux, or lib/mac subdirectories and will use MUMPS Linear Solver if these solvers are not available. HSL is the highest priority.

HSL website: http://www.hsl.rl.ac.uk/ipopt/

Pardiso website: http://www.pardiso-project.org/