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This is how I tracked my thesis writing. I will be glad if one make good use of it.

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suryamondal/PhD_Thesis

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My PhD thesis

The most important part is the bibliography, where most of us get confused. The articles/books/notes are listed in the chapters/surya_thesis.bib file.

Bibliography file is compiled with bibtex, but there is a catch. When we run pdflatex for the fist time, it creates a bunch of files where the reference to the citations are stored. At this point, pdflatex has no no idea how to fill those ? positions. Then we run bibtex. It uses those references to create a .bbl file. Then we run pdflatex again to fill the ?.

Relax, no need to get worried. It all have been taken care of in the execute.

One important advantage of bibtex is that it sorts the bibitems automatically. So one does not need to take care of the ordering of items in the .bib file when populating.

Compile with bibliography:  ./execute surya_thesis 1
                     Else:  ./execute surya_thesis

Cover Page: For book binding: This is given in titlepageCover directory.

Go to this directory and compile with: pdflatex surya_thesis.tex.