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Thanks for the thougths. That's the solution. Is there a chance I can use cygwin to run matlab (including plotting functions etc.), which is located on another machine?
I'm getting this warning Warning: No display specified. You will not be able to display graphics on the screen.
some more data ? Is the remote machine a Unix one ? If so the you can look at http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-ssh-no-x11forwarding
If it is a windows machine I doubt matlab provides a X interface usable by cygwin
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