If you are looking for batch processing, octave may be an option.  The
objective was to be as compatible with Matlab as possible.  There
wasn't any gui available when I last looked at this program.  

As a side note, I found the following from the Matlab site hilarious :
FreeBSD distributions of Linux are not compatible with MATLAB 6.0 (R12).

Makes me wonder how good the Linux version of Matlab is.
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