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As mentioned before, the Middleware takes care of timing. As soon as your script has told it that it is ready to operate, the Middleware should appear in the Timer Tab in the LCC. Then, you can start the simulation by sending a start signal (press on the start button). Of course, you need to deploy / start the simulation to start the Middleware before you start the timer (and, if you do not use the Matlab GUI, your selected Matlab script as well).