Talk:LaTeX template for PhD thesis

FAQ: glossary troubleshooting

The glossary is difficult to get started. If you are in a hurry, consider writing it by hand. Here's what I did to get it going using the nomencl package. Jakob

changed in main doc

\usepackage{nomecl}

\makenomenclature % place this before /begin

\print nomenclature

how to place a nomenclature entry

\nomenclature[zcif]{$CIF$}{Cauchy's Integral Formula} % z for abbreviations (defined in .cls)

\nomenclature[sorting]{XYZ}{description}

how to generate the files required

Execute these commands directly via the LaTeX command line, e.g. the console in TeXShop.

makeindex  filename.nlo -s path/nomencl.ist -o filename.nls<br>
nomencl.ist = index style file

e.g. with full paths on my systems:<br>
/usr/local/gwTeX/bin/powerpc-apple-darwin7.9.0/makeindex thesis.nlo -s /usr/local/gwTeX/texmf.texlive/makeindex/nomencl/nomencl.ist -o thesis.nls

or define TexShop engine: ~/Library/TexShop/Engines/Nomencl.engine<br>
makeindex  "${1%%.tex}.nlo" -s /usr/local/gwTeX/texmf.texlive/makeindex/nomencl/nomencl.ist -o "${1%%.tex}.nls"<br>
chmod u+x Nomencl.engine

FAQ: glossary, quick work-around

If you don't want to bother with the above to get nomencl package to work, just do the glossary by hand. You will lose the ability to define glossary words at any position in the text but may save yourself some time.

\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]  produces a 2 column page for a compact glossary
\begin{footnotesize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)

BAC - bacterial artificial chromosome; circular DNA vector used to propagate large inserts in bacteria\\  % double backslash produces a free line; without it glossary entries will be directly connected but indented like paragraphs.

cDNA - complementary DNA; reverse transcribed from mRNA, essentially a DNA copy of an mRNA, usually spliced, i.e. containing exon sequences only\\

DAPI - 4’,6-diamidino-2-phenylindole; a fluorescent stain that binds strongly to DNA and serves to marks the nucleus 
in fluorescence microscopy\\

\label{nom} % target name for links to glossary

\end{footnotesize}
\end{multicols}

FAQ: empty page after section

The template appends an empty page to a section if it ends on an odd page number. This is not bug but a feature to allow all section start pages to start on an odd page, i.e. a page that faces you when you open the thesis or flip a page.