National Instruments does not recommend starting or stopping services (changing the default installed settings) as it will adversely affect the functioning of the programs installed on your machine.
You can programmatically start or stop services using the commands net start and net stop in the command prompt. For example, executing net start "NI Citadel 5" in the command prompt starts the NI Citadel 5 service.
One way to use this would be to have a batch file that has all the necessary net start or net stop commands.
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