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For those who wish to write their theses in LyX, you can use this complete example as a template provided by Dr. Mike Short. Keep the organization of the document the same, edit "cover.tex" by hand, and otherwise replace the template content with your own. Then you will have a complete document, formatted per MIT's regulations.
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Or you can just write Latex code using any text editor. I Lulu Li recommend taking advantage of the command \newcommand{command}{definition}. This allows you to save time on some commonly used definitions. See examples at here, or run:
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In particular, the mitthesis.cls file (link here) is what I Lulu used for my MS thesis (link). You should not need to update anything and use it directly.touch mitthesis.cls at all, and the master.tex is pretty self-explanatory.