To run a program in Logisim, right-click on the "Stored program" EEPROM > "Load memory image" and select your file (will probably be named something like PINEAPPLE_program_logisim). The EEPROM will now fill with data and we can run it by clicking on "Simulate" > "Auto-Tick enabled". If the clock speed is too slow or too fast, click on the "Auto-Tick frequency" in the same context menu and select your desired speed.