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From my understanding, NetBeans uses the CREF executable from the JCDK for simulation. You can check the documentation (developer guide etc) from the JCDK for more details. The CREF emulator uses a custom applet loader so it does not use standard GP commands and will be different to a real card. As for loading your applet, you should be able to run from NB and it will start your emulator and deploy your code. I do not use netbeans so cannot really comment further.