I wrote this sentence
The software consists of a graphical user interface (by /in /on/ through/ using) which the user (performs/ takes/ does) some spelling tests on a given list of words.
The bold words are those that I don't know the suitable one.
What is the correct preposition for things done through a software user interface (Ironically, I myself use through in this sentence of question)
Based on the slightly formal language you're using in the rest of the sentence:
The software consists of a graphical user interface through which the user takes some spelling tests on a given list of words.
Through as in the software is the means of performing the action.
The second part of the sentence, "Take a test" is the usual form, but you may want to consider, "through which the user is tested on their spelling with a given list of words." as an alternative that fits more with the general tone.
It's enough to say:
The software consists of a graphical user interface, on which the user can take spelling tests.
Otherwise, you can be more wordy:
The software consists of a graphical user interface, on which the student is given a list of words to test his/her spelling.
