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The model simplification operation requires at least one of the two datatypes:

Zero Value Fluxes - that can be obtained following a structural analysis or performing FVA.
Equivalent fluxes.

To simplify a model access the File -> Model Simplification menu:


After this just select the project name, and which datatypes you want to use in the simplification (at least one of them is mandatory).


And that's it! Press OK and a new project will be added to the clipboard!