An elementary flux mode (EFM) is a minimal, steady‑state pathway through a metabolic network that cannot be decomposed into simpler functioning pathways.
Calculating elementary flux modes with COPASI is straightforward. To begin, select Tasks → Stoichiometric Analysis → Elementary Modes in the object tree, then click the Run button in the dialog window that appears.
The resulting elementary modes will be shown directly in this dialog. Each elementary mode displays the reactions it contains, along with their chemical equations.
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| Elementary Flux Modes Analysis Dialog with Results |
If you wish to save the output from your Elementary Mode analysis, you will need to create an output definition. Instructions for this can be found in the Manual Definition section. The simplest method is to use the Output Assistant, which you can open using the Output Assistant button. More details are available in the Output Assistant section.
To write the analysis results to a specific file, connect the output definition to a file. Click the Report button to open a dialog that allows you to link the report from your specific task to a location on your computer. First, select a report appropriate for Elementary Flux Modes from the drop-down menu at the top. Then, click the Browse button and choose your desired destination. By default, COPASI will create a new file if it does not exist or overwrite the file if it does. Alternatively, you can choose to append the results to an existing file by selecting the Append checkbox at the bottom of the dialog.
Once you are finished, click Confirm. The next time you run the task, COPASI will write the output to the file you specified.
