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Windows Front-end

Hello all,
I'm developing a GUI front-end in Windows to manage a linux box, but I'm not sure how to connect this GUI with the linux box.
I mean, for instance, I want manage:
   -- Stop iptables,
   -- Start iptables,
   -- Flush a iptables configuration,
   -- etc, ....
Is there any protocol which control this ?
or does anyone have any suggestion ?

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