What generated your GCD file? The fileformat in 7120db.dat in http://www.people.vcu.edu/~elhaij/IntroBioinf/Programs/context/binary6.html and your format look very different and incompatible. 7129db.dat looks like fixed length records, this looks like binary tree data/something similar to a MS Word Document. I'm going to say you probably want to use OLE or a DLL supplied by the vendor of your lab equipment to decode this, unless someone in the FOSS/linux world already reverse engineered the file format, or the format is an open standard.

edit: your GCD file looks very similar to a MS Word file, the beginning of the first line of a DOC file is "ÐÏࡱá >  þÿ" the beginning of the first line of your GCD file is "ÐÏࡱá >  þÿ". Hmm, your file is a "Compound Binary File" http://en.wikipedia.org/wiki/Compound_File_Binary_Format. CPAN does have a couple module I see for parsing this, http://cpan.uwinnipeg.ca/dist/OLE/ and Finnigan::OLE2File you can try.. Again, there is probable an OLE library supplied with whatever made your GCD file that will let you programatically analyze it which is the easiest way to do it.