Entered a thesis template

thesis_template/PhDtemplateLATEX/0_frontmatter/abstract.tex

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+
+% Thesis Abstract -----------------------------------------------------
+
+
+%\begin{abstractslong}    %uncommenting this line, gives a different abstract heading
+\begin{abstracts}        %this creates the heading for the abstract page
+
+Put your abstract or summary here, if your university requires it.
+
+\end{abstracts}
+%\end{abstractlongs}
+
+
+% ---------------------------------------------------------------------- 

thesis_template/PhDtemplateLATEX/0_frontmatter/acknowledgement.tex

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+% Thesis Acknowledgements ------------------------------------------------
+
+
+%\begin{acknowledgementslong} %uncommenting this line, gives a different acknowledgements heading
+\begin{acknowledgements}      %this creates the heading for the acknowlegments
+
+I would like to acknowledge the thousands of individuals who have coded for the LaTeX project for free. It is due to their efforts that we can generate professionally typeset PDFs now.
+
+\end{acknowledgements}
+%\end{acknowledgmentslong}
+
+% ------------------------------------------------------------------------
+
+

thesis_template/PhDtemplateLATEX/0_frontmatter/dedication.tex

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+% Thesis Dedictation ---------------------------------------------------
+
+\begin{dedication} %this creates the heading for the dedication page
+
+To ...
+
+\end{dedication}
+
+% ----------------------------------------------------------------------

thesis_template/PhDtemplateLATEX/0_frontmatter/glossary.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+% Glossary entries are defined with the command \nomenclature{1}{2}
+% 1 = Entry name, e.g. abbreviation; 2 = Explanation
+% You can place all explanations in this separate file or declare them in the middle of the text. Either way they will be collected in the glossary.
+
+% required to print nomenclature name to page header
+\markboth{\MakeUppercase{\nomname}}{\MakeUppercase{\nomname}}
+
+
+% ----------------------- contents from here ------------------------
+
+% chemicals
+\nomenclature{DAPI}{4',6-diamidino-2-phenylindole; a fluorescent stain that binds strongly to DNA and serves to marks the nucleus in fluorescence microscopy} 
+\nomenclature{DEPC}{diethyl-pyro-carbonate; used to remove RNA-degrading enzymes (RNAases) from water and laboratory utensils}
+\nomenclature{DMSO}{dimethyl sulfoxide; organic solvent, readily passes through skin, cryoprotectant in cell culture}
+\nomenclature{EDTA}{Ethylene-diamine-tetraacetic acid; a chelating (two-pronged) molecule used to sequester most divalent (or trivalent) metal ions, such as calcium (Ca$^{2+}$) and magnesium (Mg$^{2+}$), copper (Cu$^{2+}$), or iron (Fe$^{2+}$ / Fe$^{3+}$)}
+
+
+

thesis_template/PhDtemplateLATEX/1_introduction/introduction.tex

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+
+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- introduction file header -----------------------
+\chapter{Introduction}
+
+% the code below specifies where the figures are stored
+\ifpdf
+    \graphicspath{{1_introduction/figures/PNG/}{1_introduction/figures/PDF/}{1_introduction/figures/}}
+\else
+    \graphicspath{{1_introduction/figures/EPS/}{1_introduction/figures/}}
+\fi
+
+% ----------------------------------------------------------------------
+%: ----------------------- introduction content ----------------------- 
+% ----------------------------------------------------------------------
+
+
+
+%: ----------------------- HELP: latex document organisation
+% the commands below help you to subdivide and organise your thesis
+%    \chapter{}       = level 1, top level
+%    \section{}       = level 2
+%    \subsection{}    = level 3
+%    \subsubsection{} = level 4
+% note that everything after the percentage sign is hidden from output
+
+
+
+\section{put section name here} % section headings are printed smaller than chapter names
+% intro
+Write your text without any further commands, like this:.... Any organised system requires energy, be it a machine of some kind or a live organism. Energy is needed to win the uphill battle against entropy and pull together lifeless molecules to be able to do something in this world, like complete a PhD.
+
+
+
+\subsection{Name your subsection} % subsection headings are again smaller than section names
+% lead
+Different organised systems have different energy currencies. The machines that enable us to do science like sizzling electricity but at a controlled voltage. Earth's living beings are no different, except that they have developed another preference. They thrive on various chemicals. 
+
+% dextran, starch, glycogen
+Most organisms use polymers of glucose units for energy storage and differ only slightly in the way they link together monomers to sometimes gigantic macromolecules. Dextran of bacteria is made from long chains of $\alpha$-1,6-linked glucose units. 
+
+%: ----------------------- HELP: special characters
+% above you can see how special characters are coded; e.g. $\alpha$
+% below are the most frequently used codes:
+%$\alpha$  $\beta$  $\gamma$  $\delta$
+
+%$^{chars to be superscripted}$  OR $^x$ (for a single character)
+%$_{chars to be suberscripted}$  OR $_x$
+
+%>  $>$  greater,  <  $<$  less
+%≥  $\ge$  greater than or equal, ≤  $\ge$  lesser than or equal
+%~  $\sim$  similar to
+
+%$^{\circ}$C   ° as in degree C
+%±  \pm     plus/minus sign
+
+%$\AA$     produces  Å (Angstrom)
+
+
+
+
+% dextran, starch, glycogen continued
+Starch of plants and glycogen of animals consists of $\alpha$-1,4-glycosidic glucose polymers \cite{lastname07}. See figure \ref{largepotato} for a comparison of glucose polymer structure and chemistry. 
+
+Two references can be placed separated by a comma \cite{lastname07,name06}.
+
+%: ----------------------- HELP: references
+% References can be links to figures, tables, sections, or references.
+% For figures, tables, and text you define the target of the link with \label{XYZ}. Then you call cross-link with the command \ref{XYZ}, as above
+% Citations are bound in a very similar way with \cite{XYZ}. You store your references in a BibTex file with a programme like BibDesk.
+
+
+
+
+
+\figuremacro{largepotato}{A common glucose polymers}{The figure shows starch granules in potato cells, taken from \href{http://molecularexpressions.com/micro/gallery/burgersnfries/burgersnfries4.html}{Molecular Expressions}.}
+
+%: ----------------------- HELP: adding figures with macros
+% This template provides a very convenient way to add figures with minimal code.
+% \figuremacro{1}{2}{3}{4} calls up a series of commands formating your image.
+% 1 = name of the file without extension; PNG, JPEG is ok; GIF doesn't work
+% 2 = title of the figure AND the name of the label for cross-linking
+% 3 = caption text for the figure
+
+%: ----------------------- HELP: www links
+% You can also see above how, www links are placed
+% \href{http://www.something.net}{link text}
+
+\figuremacroW{largepotato}{Title}{Caption}{0.8}
+% variation of the above macro with a width setting
+% \figuremacroW{1}{2}{3}{4}
+% 1-3 as above
+% 4 = size relative to text width which is 1; use this to reduce figures
+
+
+
+
+Insulin stimulates the following processes:
+
+\begin{itemize}
+\item muscle and fat cells remove glucose from the blood,
+\item cells breakdown glucose via glycolysis and the citrate cycle, storing its energy in the form of ATP,
+\item liver and muscle store glucose as glycogen as a short-term energy reserve,
+\item adipose tissue stores glucose as fat for long-term energy reserve, and
+\item cells use glucose for protein synthesis.
+\end{itemize}
+
+%: ----------------------- HELP: lists
+% This is how you generate lists in LaTeX.
+% If you replace {itemize} by {enumerate} you get a numbered list.
+
+
+ 
+
+
+%: ----------------------- HELP: tables
+% Directly coding tables in latex is tiresome. See below.
+% I would recommend using a converter macro that allows you to make the table in Excel and convert them into latex code which you can then paste into your doc.
+% This is the link: http://www.softpedia.com/get/Office-tools/Other-Office-Tools/Excel2Latex.shtml
+% It's a Excel template file containing a macro for the conversion.
+
+\begin{table}[htdp]
+\centering
+\begin{tabular}{ccc} % ccc means 3 columns, all centered; alternatives are l, r
+
+{\bf Gene} & {\bf GeneID} & {\bf Length} \\ 
+% & denotes the end of a cell/column, \\ changes to next table row
+\hline % draws a line under the column headers
+
+human latexin & 1234 & 14.9 kbps \\
+mouse latexin & 2345 & 10.1 kbps \\
+rat latexin   & 3456 & 9.6 kbps \\
+% Watch out. Every line must have 3 columns = 2x &. 
+% Otherwise you will get an error.
+
+\end{tabular}
+\caption[title of table]{\textbf{title of table} - Overview of latexin genes.}
+% You only need to write the title twice if you don't want it to appear in bold in the list of tables.
+\label{latexin_genes} % label for cross-links with \ref{latexin_genes}
+\end{table}
+
+
+
+% There you go. You already know the most important things.
+
+
+% ----------------------------------------------------------------------
+
+
+

thesis_template/PhDtemplateLATEX/2/aims.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+\chapter{Aims of the project} % top level followed by section, subsection
+
+
+% ----------------------- contents from here ------------------------
+
+\section{Final aim}
+
+Our ultimate goal is...
+
+\section{Preliminary aims}
+
+There will be several preliminary scientific targets to be accomplished on the way...
+
+
+
+
+% ---------------------------------------------------------------------------
+% ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------

thesis_template/PhDtemplateLATEX/3/subdoc.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- name of chapter  -------------------------
+\chapter{chaptername} % top level followed by section, subsection
+
+
+%: ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{X/figures/PNG/}{X/figures/PDF/}{X/figures/}}
+\else
+    \graphicspath{{X/figures/EPS/}{X/figures/}}
+\fi
+
+%: ----------------------- contents from here ------------------------
+
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+

thesis_template/PhDtemplateLATEX/4/subdoc.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- name of chapter  -------------------------
+\chapter{chaptername} % top level followed by section, subsection
+
+
+%: ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{X/figures/PNG/}{X/figures/PDF/}{X/figures/}}
+\else
+    \graphicspath{{X/figures/EPS/}{X/figures/}}
+\fi
+
+%: ----------------------- contents from here ------------------------
+
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+

thesis_template/PhDtemplateLATEX/5/subdoc.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- name of chapter  -------------------------
+\chapter{chaptername} % top level followed by section, subsection
+
+
+%: ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{X/figures/PNG/}{X/figures/PDF/}{X/figures/}}
+\else
+    \graphicspath{{X/figures/EPS/}{X/figures/}}
+\fi
+
+%: ----------------------- contents from here ------------------------
+
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+

thesis_template/PhDtemplateLATEX/6/subdoc.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- name of chapter  -------------------------
+\chapter{chaptername} % top level followed by section, subsection
+
+
+%: ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{X/figures/PNG/}{X/figures/PDF/}{X/figures/}}
+\else
+    \graphicspath{{X/figures/EPS/}{X/figures/}}
+\fi
+
+%: ----------------------- contents from here ------------------------
+
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+

thesis_template/PhDtemplateLATEX/7/discussion.tex

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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+\chapter{Discussion} % top level followed by section, subsection
+
+
+% ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{7/figures/PNG/}{7/figures/PDF/}{7/figures/}}
+\else
+    \graphicspath{{7/figures/EPS/}{7/figures/}}
+\fi
+
+
+% ----------------------- contents from here ------------------------
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+% ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------

thesis_template/PhDtemplateLATEX/8/materials_methods.tex

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+
+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+\chapter{Materials \& methods} % top level followed by section, subsection
+
+
+% ----------------------- paths to graphics ------------------------
+
+% change according to folder and file names
+\ifpdf
+    \graphicspath{{8/figures/PNG/}{8/figures/PDF/}{8/figures/}}
+\else
+    \graphicspath{{8/figures/EPS/}{8/figures/}}
+\fi
+
+% ----------------------- contents from here ------------------------
+
+
+
+
+ 
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+
+
+
+ 
+
+
+
+
+
+

thesis_template/PhDtemplateLATEX/9_backmatter/declaration.tex

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+
+% Thesis statement of originality -------------------------------------
+
+% Depending on the regulations of your faculty you may need a declaration like the one below. This specific one is from the medical faculty of the university of Dresden.
+
+\begin{declaration}        %this creates the heading for the declaration page
+
+I herewith declare that I have produced this paper without the prohibited assistance of third parties and without making use of aids other than those specified; notions taken over directly or indirectly from other sources have been identified as such. This paper has not previously been presented in identical or similar form to any other German or foreign examination board.
+
+The thesis work was conducted from XXX to YYY under the supervision of PI at ZZZ.
+
+\vspace{10mm}
+
+CITY,
+
+
+\end{declaration}
+
+
+% ----------------------------------------------------------------------

thesis_template/PhDtemplateLATEX/9_backmatter/references.bib

@@ -0,0 +1,23 @@
+
+%% Created for Jakob Suckale at 2007-09-06 11:30:44 +0200 
+
+
+%% Saved with string encoding Unicode (UTF-8) 
+
+
+
+@article{name06,
+	Author = {Name},
+	Date-Added = {2007-09-06 11:30:06 +0200},
+	Date-Modified = {2007-09-06 11:30:42 +0200},
+	Journal = {Journal of Sth},
+	Title = {Title},
+	Year = {2006}}
+
+@article{lastname07,
+	Author = {Lastname},
+	Date-Added = {2007-09-06 11:28:24 +0200},
+	Date-Modified = {2007-09-06 11:29:24 +0200},
+	Journal = {Journal of Sth},
+	Title = {Title},
+	Year = {2007}}

thesis_template/PhDtemplateLATEX/Latex/Classes/CUEDthesisPSnPDF.texshop

@@ -0,0 +1 @@
+../../thesis.tex

thesis_template/PhDtemplateLATEX/Latex/Classes/PhDthesisPSnPDF.cls

@@ -0,0 +1,409 @@
+
+%---------------------------------------------------------------
+% PhDthesis version 2 style file by Jakob Suckale, 2007
+% based on CUEDthesis version 1 by Harish Bhanderi 2002
+%---------------------------------------------------------------
+
+
+
+%-------------------------- identification ---------------------
+%\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{Latex/Classes/PhDthesisPSnPDF}[2007/09/06 v2 PhD thesis class]
+
+
+%:-------------------------- report or book -----------------------
+
+%If you want to use a Report style document then uncomment the following 3 lines and comment the below 8 book style lines:
+%\DeclareOption*{\PassOptionsToClass{\CurrentOption}{report}}
+%\ProcessOptions\relax
+%%\LoadClass[a4paper]{report}
+%\ifx\pdfoutput\undefined
+%   \LoadClass[dvips, a4paper]{report}
+%\else
+%   \LoadClass[pdftex, a4paper]{report}
+%\fi
+
+%%Bibliography
+%%uncomment next line to change bibliography name to references for Report document class
+%\renewcommand{\refname}{References}
+
+%If you want to use a Book style document then uncomment the following 3 lines and comment the above 8 report style lines:
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{book}}
+\ProcessOptions\relax
+\ifx\pdfoutput\undefined
+   \LoadClass[dvips, a4paper]{book}
+\else
+   \LoadClass[pdftex, a4paper]{book}
+\fi
+
+
+%:-------------------------- packages for fancy things -----------------------
+
+\usepackage{amssymb}
+\usepackage{graphics} % for improved inclusion of graphics
+%\usepackage{wrapfig} % to include figure with text wrapping around it
+\usepackage[margin=10pt,font=small,labelfont=bf]{caption} % for improved layout of figure captions with extra margin, smaller font than text
+\usepackage{fancyhdr} % for better header layout
+\usepackage{eucal}
+\usepackage[english]{babel}
+\usepackage[usenames, dvipsnames]{color}
+\usepackage[perpage]{footmisc}
+\usepackage[round, sort, numbers]{natbib}
+\usepackage{ifthen}
+\usepackage{multicol} % for pages with multiple text columns, e.g. References
+\setlength{\columnsep}{20pt} % space between columns; default 10pt quite narrow
+\usepackage[nottoc]{tocbibind} % correct page numbers for bib in TOC, nottoc suppresses an entry for TOC itself
+%\usepackage{nextpage}
+
+%:-------------------------- Glossary/Abbrev./Symbols -----------------------
+
+\usepackage[intoc]{nomencl} % load nomencl extension; include in TOC
+%\nomrefpage % to include page numbers after abbrevations
+\renewcommand{\nomname}{Glossary} % rename nomenclature
+\renewcommand{\nomlabel}[1]{\textbf{#1}} % make abbreviations bold
+\makenomenclature % used to be \makeglossary
+\newcommand{\g}{\footnote{For all abbreviations see the glossary on page \pageref{nom}.}} % type "\g" to refer to glossary
+
+% used to be for sorting into categories:
+%\renewcommand\nomgroup[1]{%
+%  \ifthenelse{\equal{#1}{A}}{%
+%   \item[\textbf{Roman Symbols}] }{%             A - Roman
+%    \ifthenelse{\equal{#1}{G}}{%
+%     \item[\textbf{Greek Symbols}]}{%             G - Greek
+%      \ifthenelse{\equal{#1}{R}}{%
+%        \item[\textbf{Superscripts}]}{%              R - Superscripts
+%          \ifthenelse{\equal{#1}{S}}{%
+%           \item[\textbf{Subscripts}]}{{%             S - Subscripts
+%	    \ifthenelse{\equal{#1}{X}}{%
+%	     \item[\textbf{Other Symbols}]}{{%    X - Other Symbols
+%	    \ifthenelse{\equal{#1}{Z}}{%
+%	     \item[\textbf{Acronyms}]}%              Z - Acronyms
+%              			{{}}}}}}}}}}
+
+
+%:-------------------------- PDF/PS setup -----------------------
+
+%if you use a macTeX 2008 or later, use the ifpdf package
+\usepackage{ifpdf} 
+
+%if you use an older version, uncomment these lines:
+%\newif \ifpdf
+%    \ifx \pdfoutput \undefined
+        % for running latex
+%        \pdffalse
+%    \else
+        % for running pdflatex
+%        \pdfoutput = 1    % positive value for a PDF output
+                          % otherwise a DVI
+%        \pdftrue
+%\fi
+
+\ifpdf
+%-->
+%--> Google.com search "hyperref options"
+%--> 
+%--> http://www.ai.mit.edu/lab/sysadmin/latex/documentation/latex/hyperref/manual.pdf
+%--> http://www.chemie.unibas.ch/~vogtp/LaTeX2PDFLaTeX.pdf 
+%--> http://www.uni-giessen.de/partosch/eurotex99/ oberdiek/print/sli4a4col.pdf
+%--> http://me.in-berlin.de/~miwie/tex-refs/html/latex-packages.html
+%-->
+    \usepackage[ pdftex, plainpages = false, pdfpagelabels, 
+                 pdfpagelayout = useoutlines,
+                 bookmarks,
+                 bookmarksopen = true,
+                 bookmarksnumbered = true,
+                 breaklinks = true,
+                 linktocpage,
+                 pagebackref,
+                 colorlinks = false,  % was true
+                 linkcolor = blue,
+                 urlcolor  = blue,
+                 citecolor = red,
+                 anchorcolor = green,
+                 hyperindex = true,
+                 hyperfigures
+                 ]{hyperref} 
+
+    \DeclareGraphicsExtensions{.png, .jpg, .jpeg, .pdf, .gif} %GIF doesn't work??
+    \usepackage[pdftex]{graphicx}
+    \pdfcompresslevel=9
+    \graphicspath{{0_frontmatter/figures/PNG/}{0_frontmatter/figures/PDF/}{0_frontmatter/figures/}}
+\else
+    \usepackage[ dvips, 
+                 bookmarks,
+                 bookmarksopen = true,
+                 bookmarksnumbered = true,
+                 breaklinks = true,
+                 linktocpage,
+                 pagebackref,
+                 colorlinks = true,
+                 linkcolor = blue,
+                 urlcolor  = blue,
+                 citecolor = red,
+                 anchorcolor = green,
+                 hyperindex = true,
+                 hyperfigures
+                 ]{hyperref}
+
+    \DeclareGraphicsExtensions{.eps, .ps}
+    \usepackage{epsfig}
+    \usepackage{graphicx}
+    \graphicspath{{0_frontmatter/figures/EPS/}{0_frontmatter/figures/}}
+\fi
+
+
+%:-------------------------- page layout -----------------------
+
+%A4 settings
+\ifpdf
+   \pdfpageheight=297mm
+   \pdfpagewidth=210mm
+\else
+   \setlength{\paperheight}{297mm}
+   \setlength{\paperwidth}{210mm}
+\fi
+
+\setlength{\hoffset}{0.00cm}
+\setlength{\voffset}{0.00cm}
+
+%: Uncomment this secion for two-sided printing
+% ------------------------------
+\setlength{\oddsidemargin}{1.5cm}
+\setlength{\evensidemargin}{0cm}
+\setlength{\topmargin}{1mm}
+\setlength{\headheight}{1.36cm}
+\setlength{\headsep}{1.00cm}
+\setlength{\textheight}{20.84cm}
+\setlength{\textwidth}{14.5cm}
+\setlength{\marginparsep}{1mm}
+\setlength{\marginparwidth}{3cm}
+\setlength{\footskip}{2.36cm}
+
+
+%: Uncomment this secion for one-sided printing
+% taken from the original file, but with the first two lanes modified
+% ------------------------------
+%\setlength{\evensidemargin}{1.9cm} % was 1.96cm in original
+%\setlength{\oddsidemargin}{-0.001cm} % was -0.54cm in original file
+%\setlength{\topmargin}{1mm}
+%\setlength{\headheight}{1.36cm}
+%\setlength{\headsep}{1.00cm}
+%\setlength{\textheight}{20.84cm}
+%\setlength{\textwidth}{14.5cm}
+%\setlength{\marginparsep}{1mm}
+%\setlength{\marginparwidth}{3cm}
+%\setlength{\footskip}{2.36cm}
+
+
+%: section below defines fancy page layout options
+% ------------------------------
+\pagestyle{fancy}
+\renewcommand{\chaptermark}[1]{\markboth{\MakeUppercase{\thechapter. #1 }}{}}
+\renewcommand{\sectionmark}[1]{\markright{\thesection\ #1}}
+\fancyhf{}
+\fancyhead[RO]{\bfseries\rightmark}
+\fancyhead[LE]{\bfseries\leftmark}
+\fancyfoot[C]{\thepage}
+\renewcommand{\headrulewidth}{0.5pt}
+\renewcommand{\footrulewidth}{0pt}
+\addtolength{\headheight}{0.5pt}
+\fancypagestyle{plain}{
+  \fancyhead{}
+  \renewcommand{\headrulewidth}{0pt}
+}
+
+
+
+
+
+%:-------------------------- title page layout -----------------------
+
+% starts roman page numbering until chapter 1
+% important to avoid two pages numbered 1 and 2 which may cause bad links
+% bug: cover i + back side ii and then numbering restarts with i; should be iii
+\renewcommand{\thepage}{\roman{page}}
+
+\newcommand{\submittedtext}{{A thesis submitted for the degree of}}
+
+% DECLARATIONS
+% These macros are used to declare arguments needed for the
+% construction of the title page and other preamble.
+
+% The year and term the degree will be officially conferred
+\def\degreedate#1{\gdef\@degreedate{#1}}
+% The full (unabbreviated) name of the degree
+\def\degree#1{\gdef\@degree{#1}}
+% The name of your college or department(eg. Trinity, Pembroke, Maths, Physics)
+\def\collegeordept#1{\gdef\@collegeordept{#1}}
+% The name of your University
+\def\university#1{\gdef\@university{#1}}
+% Defining the crest
+\def\crest#1{\gdef\@crest{#1}}
+% Stating the city of birth for title page where needed; uncommented for use
+%\def\cityofbirth#1{\gdef\@cityofbirth{#1}}
+
+% These macros define an environment for front matter that is always 
+% single column even in a double-column document.
+
+\newenvironment{alwayssingle}{%
+       \@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn
+       \else\newpage\fi}
+       {\if@restonecol\twocolumn\else\newpage\fi}
+
+%define title page layout
+\renewcommand{\maketitle}{%
+\begin{alwayssingle}
+    \renewcommand{\footnotesize}{\small}
+    \renewcommand{\footnoterule}{\relax}
+    \thispagestyle{empty}
+%  \null\vfill
+  \begin{center}
+    { \Huge {\bfseries {\@title}} \par}
+{\large \vspace*{35mm} {{\@crest} \par} \vspace*{25mm}}
+    {{\Large \@author} \par}
+%	\vspace*{1ex}
+%	{{\@cityofbirth} \par}    
+{\large 
+	\vspace*{1ex}
+    {{\@collegeordept} \par}
+	\vspace*{1ex}
+    {{\@university} \par}
+	\vspace*{25mm}
+    {{\submittedtext} \par}
+	\vspace*{1ex}
+    {\it {\@degree} \par}
+	\vspace*{2ex}
+    {\@degreedate}
+}%end large
+  \end{center}
+  \null\vfill
+\end{alwayssingle}}
+
+% page number for cover back side should have page number blanked
+
+
+%:-------------------------- front matter layout -----------------------
+
+% DEDICATION
+%
+% The dedication environment makes sure the dedication gets its
+% own page and is set out in verse format.
+
+\newenvironment{dedication}
+{\begin{alwayssingle}
+  \pagestyle{empty}
+  \begin{center}
+  \vspace*{1.5cm}
+  {\LARGE }
+  \end{center}
+  \vspace{0.5cm}
+  \begin{quote} \begin{center}}
+{\end{center} \end{quote} \end{alwayssingle}}
+
+
+% ACKNOWLEDGEMENTS
+%
+% The acknowledgements environment puts a large, bold, centered 
+% "Acknowledgements" label at the top of the page. The acknowledgements
+% themselves appear in a quote environment, i.e. tabbed in at both sides, and
+% on its own page.
+
+\newenvironment{acknowledgements}
+{\pagestyle{empty}
+\begin{alwayssingle}
+\begin{center}
+\vspace*{1.5cm}
+{\Large \bfseries Acknowledgements}
+\end{center}
+\vspace{0.5cm}
+\begin{quote}}
+{\end{quote}\end{alwayssingle}}
+
+% The acknowledgementslong environment puts a large, bold, centered 
+% "Acknowledgements" label at the top of the page. The acknowledgement itself 
+% does not appears in a quote environment so you can get more in.
+
+\newenvironment{acknowledgementslong}
+{\pagestyle{empty}
+\begin{alwayssingle}
+\begin{center}
+\vspace*{1.5cm}
+{\Large \bfseries Acknowledgements}
+\end{center}
+\vspace{0.5cm}\begin{quote}}
+{\end{quote}\end{alwayssingle}}
+
+%ABSTRACT
+%
+%The abstract environment puts a large, bold, centered "Abstract" label at
+%the top of the page. The abstract itself appears in a quote environment,
+%i.e. tabbed in at both sides, and on its own page.
+
+\newenvironment{abstracts} {\begin{alwayssingle} \pagestyle{empty}
+  \begin{center}
+  \vspace*{1.5cm}
+  {\Large \bfseries  Abstract}
+  \end{center}
+  \vspace{0.5cm}
+   \begin{quote}}
+{\end{quote}\end{alwayssingle}}
+
+%The abstractlong environment puts a large, bold, centered "Abstract" label at
+%the top of the page. The abstract itself does not appears in a quote
+%environment so you can get more in.
+
+\newenvironment{abstractslong} {\begin{alwayssingle} \pagestyle{empty}
+  \begin{center}
+  \vspace*{1.5cm}
+  {\Large \bfseries  Abstract}
+  \end{center}
+  \vspace{0.5cm} \begin{quote}}
+{\end{quote}\end{alwayssingle}}
+
+%The abstractseparate environment is for running of a page with the abstract
+%on including title and author etc as required to be handed in separately
+
+\newenvironment{abstractseparate} {\begin{alwayssingle} \pagestyle{empty}
+  \vspace*{-1in}
+ \begin{center}
+    { \Large {\bfseries {\@title}} \par}
+    {{\large \vspace*{1ex} \@author} \par}
+{\large \vspace*{1ex}
+    {{\@collegeordept} \par}
+    {{\@university} \par}
+\vspace*{1ex}
+    {{\it \submittedtext} \par}
+    {\it {\@degree} \par}
+\vspace*{2ex}
+    {\@degreedate}}
+  \end{center}}
+{\end{alwayssingle}}
+
+%Statement of originality if required
+
+\newenvironment{declaration} {\begin{alwayssingle} \pagestyle{empty}
+  \begin{center}
+  \vspace*{1.5cm}
+  {\Large \bfseries  Declaration}
+  \end{center}
+  \vspace{0.5cm}
+   \begin{quote}}
+{\end{quote}\end{alwayssingle}}
+
+
+%:-------------------------- page numbers: roman+arabic -----------------------
+
+% ROMANPAGES
+%
+% The romanpages environment set the page numbering to lowercase roman one
+% for the contents and figures lists. It also resets
+% page-numbering for the remainder of the dissertation (arabic, starting at 1).
+
+%\newenvironment{romanpages}
+%{
+%	\setcounter{page}{1}
+%	\renewcommand{\thepage}{\roman{page}}
+%} % close romanpage env't
+ 
+{\newpage\renewcommand{\thepage}{\arabic{page}}\setcounter{page}{1}}
+

thesis_template/PhDtemplateLATEX/Latex/Classes/urlbst

@@ -0,0 +1,676 @@
+#! /usr/bin/env perl
+#
+# Usage: ./urlbst.pl [--eprint] [--doi]
+#    [--nohyperlinks] [--inlinelinks] [--hypertex] [--hyperref]
+#    [input-file [output-file]]
+# If either input-file or output-file is omitted, they are replaced by
+# stdin or stdout respectively.
+#
+# See http://purl.org/nxg/dist/urlbst for documentation
+#
+# $Id: urlbst.in,v 1.8 2007/03/26 17:21:56 norman Exp $
+
+$version = '0.6';
+($progname = $0) =~ s/.*\///;
+$mymarker = "% $progname";
+$mymarkerend = "% ...$progname to here";
+$myurl = 'http://purl.org/nxg/dist/urlbst';
+
+
+$infile = '-';
+$outfile = '-';
+
+$addeprints = 0;     # if true (nonzero) we add support for eprints
+$eprintprefix = 'arXiv:';	# make these settable with --eprint? syntax?
+$eprinturl = 'http://arxiv.org/abs/';
+
+$adddoiresolver = '0';
+$doiprefix = 'doi:';
+$doiurl = 'http://dx.doi.org/';
+
+$makehref = 0;
+$availablestring = "Available from: ";
+$inlinelinks = 0;
+
+$Usage = "$progname [--eprint] [--doi]\n    [--nohyperlinks] [--inlinelinks] [--hypertex] [--hyperref]\n    [--help] [input-file [output-file]]";
+
+while ($#ARGV >= 0) {
+    if ($ARGV[0] eq '--eprint') {
+	$addeprints = 1;
+    } elsif ($ARGV[0] eq '--doi') {
+        $adddoiresolver = 1;
+    } elsif ($ARGV[0] eq '--nohyperlinks') {
+        $makehref = 0;
+    } elsif ($ARGV[0] eq '--hypertex') {
+	$makehref = 1;
+    } elsif ($ARGV[0] eq '--hyperref') {
+	$makehref = 2;
+    } elsif ($ARGV[0] eq '--inlinelinks') {
+        $inlinelinks = 1;
+    } elsif ($ARGV[0] eq '--help') {
+        print <<EOD;
+urlbst version $version
+    Usage: $Usage
+      --eprint:       include support for `eprint' fields
+      --doi:          include support for `doi' field
+      --nohyperlinks  do not include active links anywhere
+      --inlinelinks   add hyperlinks to entry titles
+      --hypertex:     include HyperTeX-style hyperlink support
+      --hyperref:     include {hyperref}-style hyperlink support
+                      (generally better)
+      --help:         print this help
+    Input and output files may be given as `-' (default) to indicate stdin/out
+EOD
+        exit(0);
+    } elsif ($ARGV[0] =~ /^-/) {
+        die "Unrecognised option $ARGV[0]: Usage: $Usage\n";
+    } elsif ($infile eq '-') {
+	$infile = $ARGV[0];
+    } elsif ($outfile eq '-') {
+	$outfile = $ARGV[0];
+    } else {
+	die "Usage: $Usage\n";
+    }
+    shift(@ARGV);
+}
+
+if ($inlinelinks && $makehref == 0) {
+    print <<'EOD';
+Warning: --inlinelinks and --nohyperlinks were both specified (possibly
+    implicitly).  That combination makes no sense, so I'll ignore
+    --nohyperlinks and use --hyperref instead
+EOD
+    $makehref = 2;
+}
+
+$exitstatus = 0;		# success status
+
+open (IN, "<$infile") || die "Can't open $infile to read";
+open (OUT, ">$outfile") || die "Can't open $outfile to write";
+
+# We have to make certain assumptions about the source files, in order
+# to patch them at the correct places.  Specifically, we assume that
+#
+#   - there's a function init.state.consts
+#
+#   - ...and an output.nonnull which does the actual outputting, which
+#         has the `usual' interface.
+#
+#   - we can replace
+#           fin.entry
+#       by
+#           new.block
+#           output.url    % the function which formats and displays any URL
+#           fin.entry
+#
+#   - there is a function which handles the `article' entry type (this
+#         will always be true)
+#
+#   - there is a function output.bibitem which is called at the
+#         beginning of each entry type
+#   - ...and one called fin.entry which is called at the end
+#
+# If the functions format.date, format.title or new.block are not defined (the
+# former is not in apalike, for example, and the last is not in the
+# AMS styles), then replacements are included in the output.
+#
+# All these assumptions are true of the standard files and, since most
+# style files derive from them more or less directly, are true of most (?)
+# other style files, too.
+#
+# There's some rather ugly Perl down here.  The parsing for
+# brace-matching could probably do with being rewritten in places, to
+# make it less ugly, and more robust.
+
+print OUT "%%% Modification of BibTeX style file ", ($infile eq '-' ? '<stdin>' : $infile), "\n";
+print OUT "%%% ... by $progname, version $version (marked with \"$mymarker\")\n%%% See <$myurl>\n";
+print OUT "%%% Added webpage entry type, and url and lastchecked fields.\n";
+print OUT "%%% Added eprint support.\n"   if ($addeprints);
+print OUT "%%% Added DOI support.\n"      if ($adddoiresolver);
+print OUT "%%% Added HyperTeX support.\n" if ($makehref == 1);
+print OUT "%%% Added hyperref support.\n" if ($makehref == 2);
+print OUT "%%% Original headers follow...\n\n";
+
+$found{initconsts} = 0;
+$found{outputnonnull} = 0;
+$found{article} = 0;
+$found{outputbibitem} = 0;
+$found{finentry} = 0;
+$found{formatdate} = 0;
+$found{formattitle} = 0;
+$found{newblock} = 0;
+
+while (<IN>) {
+    /^ *%/ && do {
+        # Pass commented lines unchanged
+        print OUT;
+        next;
+    };
+    
+    /^ *ENTRY/ && do {
+	# Work through the list of entry types, finding what ones are there.
+	# If we find a URL entry there already, object, since these edits
+	# will mess things up.
+	$line = $_;
+	until ($line =~ /\{\s*(\w*)/) {
+	    $line .= <IN>;
+	}
+	$bracematchtotal = 0;	# reset
+	bracematcher($line);
+	$line =~ /\{\s*(\w*)/;
+	$found{'entry'.$1} = 1;
+	print OUT $line;
+	$line = <IN>;
+	until (bracematcher($line) == 0) {
+	    # XXX deal with multiple entries on one line
+	    ($line =~ /^\s*(\w*)/) && ($found{'entry'.$1} = 1);
+	    print OUT $line;
+	    $line = <IN>;
+	}
+	if (defined($found{entryurl})) {
+	    print STDERR "$progname: style file $infile already has URL entry!\n";
+	    # print out the rest of the file, and give up
+            print OUT $line;
+	    while (<IN>) {
+		print OUT;
+	    }
+	    $exitstatus = 1;
+	    last;
+	} else {
+            print OUT "    eprint $mymarker\n    doi $mymarker\n    url $mymarker\n    lastchecked $mymarker\n";
+	}
+	print OUT $line;
+	next;
+    };
+
+    /^ *FUNCTION *\{init\.state\.consts\}/ && do {
+        # In the init.state.consts function, add an extra set of
+        # constants at the beginning.  Also use this as the marker for
+        # the place to add the init strings function.
+        print OUT <<EOD;
+STRINGS { urlintro eprinturl eprintprefix doiprefix doiurl openinlinelink closeinlinelink } $mymarker...
+INTEGERS { hrefform inlinelinks makeinlinelink addeprints adddoiresolver }
+% Following constants may be adjusted by hand, if desired
+FUNCTION {init.urlbst.variables}
+{
+  "$availablestring" 'urlintro := % prefix before URL
+  "$eprinturl" 'eprinturl := % prefix to make URL from eprint ref
+  "$eprintprefix" 'eprintprefix := % text prefix printed before eprint ref
+  "$doiurl" 'doiurl := % prefix to make URL from DOI
+  "$doiprefix" 'doiprefix :=      % text prefix printed before DOI ref
+  #$addeprints 'addeprints :=         % 0=no eprints; 1=include eprints
+  #$adddoiresolver 'adddoiresolver :=     % 0=no DOI resolver; 1=include it
+  #$makehref 'hrefform :=           % 0=no crossrefs; 1=hypertex xrefs; 2=hyperref refs
+  #$inlinelinks 'inlinelinks :=        % 0=URLs explicit; 1=URLs attached to titles
+  % the following are internal state variables, not config constants
+  #0 'makeinlinelink :=     % state variable managed by setup.inlinelink
+  "" 'openinlinelink :=     % ditto
+  "" 'closeinlinelink :=    % ditto
+}
+INTEGERS { 
+  bracket.state
+  outside.brackets
+  open.brackets
+  within.brackets
+  close.brackets
+}
+$mymarkerend
+EOD
+	$line = $_;
+	until ($line =~ /\{.*\}.*\{/s) {
+	    $line .= <IN>;
+	}
+	$line =~ s/(\{.*?\}.*?\{)/$1 #0 'outside.brackets := $mymarker
+  #1 'open.brackets :=
+  #2 'within.brackets :=
+  #3 'close.brackets :=
+
+ /s;
+	print OUT $line;
+	$found{initconsts} = 1;
+	next;
+    };
+
+    /^ *EXECUTE *\{init\.state\.consts\}/ && do {
+        print OUT "EXECUTE {init.urlbst.variables}\n";
+        print OUT;
+        next;
+    };
+
+    /^ *FUNCTION *\{new.block\}/ && do {
+        $found{newblock} = 1;
+    };
+
+    /^ *FUNCTION *{output\.nonnull}/ && do {
+	print OUT "$mymarker\n";
+	print OUT "FUNCTION {output.nonnull.original}\n";
+        copy_block();
+	print_output_functions();
+	$found{outputnonnull} = 1;
+	next;
+    };
+
+    /FUNCTION *\{fin.entry\}/ && do {
+        # Rename fin.entry to fin.entry.original (wrapped below)
+        s/fin.entry/fin.entry.original/;
+        $found{finentry} = 1;
+        print OUT;
+        next;
+    };
+
+    /^ *FUNCTION *{format\.date}/ && do {
+	$found{formatdate} = 1;
+	print OUT;
+	next;
+    };
+
+    /^ *FUNCTION *{format\.title}/ && do {
+        # record that we found this
+	$found{formattitle} = 1;
+        print OUT;
+	next;
+    };
+
+    /^ *format\.b?title/ && do {
+        # interpolate a call to setup.inlinelink
+        print OUT "  title empty\$ 'skip\$ 'setup\.inlinelink if\$ $mymarker\n";
+        print OUT;
+        next;
+    };
+
+    /^ *FUNCTION *\{article\}/ && do {
+
+	print_missing_functions();
+	print_webpage_def();
+
+	print OUT;
+	$found{article} = 1;
+	next;
+    };
+
+    /FUNCTION *\{output.bibitem\}/ && do {
+        # Rename output.bibitem to output.bibitem.original (wrapped below)
+        s/{output.bibitem\}/\{output.bibitem.original\}/;
+ 	$found{outputbibitem} = 1;
+        print OUT;
+        next;
+    };
+
+    print OUT;
+};
+
+if ($exitstatus == 0) {
+    # Skip this if we've already reported an error -- it'll only be confusing
+    foreach $k (keys %found) {
+        if ($found{$k} == 0) {
+            print STDERR "$progname: $infile: failed to find feature $k\n";
+        }
+    }
+}
+
+close (IN);
+close (OUT);
+
+exit $exitstatus;;
+
+
+
+
+
+
+sub print_output_functions {
+    print OUT "$mymarker...\n";
+
+    print OUT <<'EOD';
+% The following three functions are for handling inlinelink.  They wrap
+% a block of text which is potentially output with write$ by multiple
+% other functions, so we don't know the content a priori.
+% They communicate between each other using the variables makeinlinelink
+% (which is true if a link should be made), and closeinlinelink (which holds
+% the string which should close any current link.  They can be called
+% at any time, but start.inlinelink will be a no-op unless something has
+% previously set makeinlinelink true, and the two ...end.inlinelink functions
+% will only do their stuff if start.inlinelink has previously set
+% closeinlinelink to be non-empty.
+FUNCTION {setup.inlinelink}
+{ makeinlinelink
+    { hrefform #1 = % hypertex
+        { "\special {html:<a href=" quote$ * url * quote$ * "> }{" * 'openinlinelink :=
+          "\special {html:</a>}" 'closeinlinelink :=
+          }
+        { hrefform #2 = % hyperref
+            { "\href{" url * "}{" * 'openinlinelink :=
+              "}" 'closeinlinelink :=
+              }
+            'skip$
+          if$ % hrefform #2 =
+        }
+      if$ % hrefform #1 =
+      #0 'makeinlinelink :=
+    }
+    'skip$
+ if$ % makeinlinelink
+}
+FUNCTION {add.inlinelink}
+{ openinlinelink empty$
+    'skip$
+    { openinlinelink swap$ * closeinlinelink *
+      "" 'openinlinelink :=
+      }
+  if$
+}
+EOD
+
+    # new.block is defined elsewhere
+
+    print OUT <<'EOD';
+FUNCTION {output.nonnull}
+{ % Save the thing we've been asked to output
+  's :=
+  % If the bracket-state is close.brackets, then add a close-bracket to
+  % what is currently at the top of the stack, and set bracket.state
+  % to outside.brackets
+  bracket.state close.brackets =
+    { "]" *
+      outside.brackets 'bracket.state :=
+    }
+    'skip$
+  if$
+  bracket.state outside.brackets =
+    { % We're outside all brackets -- this is the normal situation.
+      % Write out what's currently at the top of the stack, using the
+      % original output.nonnull function.
+      s
+      add.inlinelink
+      output.nonnull.original % invoke the original output.nonnull
+    }
+    { % Still in brackets.  Add open-bracket or (continuation) comma, add the
+      % new text (in s) to the top of the stack, and move to the close-brackets
+      % state, ready for next time (unless inbrackets resets it).  If we come
+      % into this branch, then output.state is carefully undisturbed.
+      bracket.state open.brackets =
+        { " [" * }
+        { ", " * } % bracket.state will be within.brackets
+      if$ 
+      s * 
+      close.brackets 'bracket.state :=
+    }
+  if$
+}
+
+% Call this function just before adding something which should be presented in 
+% brackets.  bracket.state is handled specially within output.nonnull.
+FUNCTION {inbrackets}
+{ bracket.state close.brackets =
+    { within.brackets 'bracket.state := } % reset the state: not open nor closed
+    { open.brackets 'bracket.state := }
+  if$
+}
+
+FUNCTION {format.lastchecked}
+{ lastchecked empty$
+    { "" }
+    { inbrackets "cited " lastchecked * }
+  if$
+}
+EOD
+    print OUT "$mymarkerend\n";
+}
+
+sub print_webpage_def {
+    print OUT "$mymarker...\n";
+
+    # Some of the functions below call new.block, so we need a dummy
+    # version, in the case where the style being edited doesn't supply
+    # that function.
+    if (! $found{newblock}) {
+        print OUT "FUNCTION {new.block} % dummy new.block function\n{\n  % empty\n}\n\n";
+        $found{newblock} = 1;
+    }
+
+    print OUT <<'EOD';
+% Functions for making hypertext links.
+% In all cases, the stack has (link-text href-url)
+%
+% make 'null' specials
+FUNCTION {make.href.null}
+{
+  pop$
+}
+% make hypertex specials
+FUNCTION {make.href.hypertex}
+{ 
+  "\special {html:<a href=" quote$ *
+  swap$ * quote$ * "> }" * swap$ *
+  "\special {html:</a>}" *
+}
+% make hyperref specials
+FUNCTION {make.href.hyperref}
+{ 
+  "\href {" swap$ * "} {\path{" * swap$ * "}}" *
+}
+FUNCTION {make.href}
+{ hrefform #2 =
+    'make.href.hyperref      % hrefform = 2
+    { hrefform #1 =
+        'make.href.hypertex  % hrefform = 1
+        'make.href.null      % hrefform = 0 (or anything else)
+      if$
+    }
+  if$
+}
+
+% If inlinelinks is true, then format.url should be a no-op, since it's
+% (a) redundant, and (b) could end up as a link-within-a-link.
+FUNCTION {format.url}
+{ inlinelinks #1 = url empty$ or
+   { "" }
+   { hrefform #1 =
+       { % special case -- add HyperTeX specials
+         urlintro "\url{" url * "}" * url make.href.hypertex * }
+       { urlintro "\url{" * url * "}" * }
+     if$
+   }
+  if$
+}
+
+FUNCTION {format.eprint}
+{ eprint empty$
+    { "" }
+    { eprintprefix eprint * eprinturl eprint * make.href }
+  if$
+}
+
+FUNCTION {format.doi}
+{ doi empty$
+    { "" }
+    { doiprefix doi * doiurl doi * make.href }
+  if$
+}
+
+% Output a URL.  We can't use the more normal idiom (something like
+% `format.url output'), because the `inbrackets' within
+% format.lastchecked applies to everything between calls to `output',
+% so that `format.url format.lastchecked * output' ends up with both
+% the URL and the lastchecked in brackets.
+FUNCTION {output.url}
+{ url empty$
+    'skip$ 
+    { new.block 
+      format.url output
+      format.lastchecked output 
+    }
+  if$
+}
+
+FUNCTION {output.web.refs}
+{
+  new.block
+  output.url
+  addeprints eprint empty$ not and
+    { format.eprint output.nonnull }
+    'skip$
+  if$
+  adddoiresolver doi empty$ not and
+    { format.doi output.nonnull }
+    'skip$
+  if$
+}
+
+% Wrapper for output.bibitem.original.
+% If the URL field is not empty, set makeinlinelink to be true,
+% so that an inline link will be started at the next opportunity
+FUNCTION {output.bibitem}
+{ outside.brackets 'bracket.state :=
+  output.bibitem.original
+  inlinelinks url empty$ not and
+    { #1 'makeinlinelink := }
+    { #0 'makeinlinelink := }
+  if$
+}
+
+% Wrapper for fin.entry.original
+FUNCTION {fin.entry}
+{ output.web.refs  % urlbst
+  makeinlinelink       % ooops, it appears we didn't have a title for inlinelink
+    { setup.inlinelink % add some artificial link text here, as a fallback
+      "[link]" output.nonnull }
+    'skip$
+  if$
+  bracket.state close.brackets = % urlbst
+    { "]" * }
+    'skip$
+  if$
+  fin.entry.original
+}
+
+% Webpage entry type.
+% Title and url fields required;
+% author, note, year, month, and lastchecked fields optional
+% See references 
+%   ISO 690-2 http://www.nlc-bnc.ca/iso/tc46sc9/standard/690-2e.htm
+%   http://www.classroom.net/classroom/CitingNetResources.html
+%   http://neal.ctstateu.edu/history/cite.html
+%   http://www.cas.usf.edu/english/walker/mla.html
+% for citation formats for web pages.
+FUNCTION {webpage}
+{ output.bibitem
+  author empty$
+    { editor empty$
+        'skip$  % author and editor both optional
+        { format.editors output.nonnull }
+      if$
+    }
+    { editor empty$
+        { format.authors output.nonnull }
+        { "can't use both author and editor fields in " cite$ * warning$ }
+      if$
+    }
+  if$
+  new.block
+  title empty$ 'skip$ 'setup.inlinelink if$
+  format.title "title" output.check
+  inbrackets "online" output
+  new.block
+  year empty$
+    'skip$
+    { format.date "year" output.check }
+  if$
+  % We don't need to output the URL details ('lastchecked' and 'url'),
+  % because fin.entry does that for us, using output.web.refs.  The only
+  % reason we would want to put them here is if we were to decide that
+  % they should go in front of the rather miscellaneous information in 'note'.
+  new.block
+  note output
+  fin.entry
+}
+EOD
+
+    print OUT "$mymarkerend\n\n\n";
+}
+
+
+sub print_missing_functions {
+    # We've got to the bit of the file which handles the entry
+    # types, so write out the webpage entry handler.  This uses
+    # the format.date function, which which many but not all
+    # bst files have (for example, apalike doesn't).  So
+    # check that we either have found this function already, or
+    # add it.
+    if (! $found{formatdate}) {
+	if ($found{entrymonth}) {
+	    print OUT <<'EOD';
+FUNCTION {format.date}
+{ year empty$
+    { month empty$
+	{ "" }
+	{ "there's a month but no year in " cite$ * warning$
+	  month
+	}
+      if$
+    }
+    { month empty$
+	'year
+	{ month " " * year * }
+      if$
+    }
+  if$
+}
+EOD
+	} else {
+	    print OUT <<'EOD';
+FUNCTION {format.date}
+{ year empty$
+    'skip$
+    { %write$
+      "(" year * ")" *
+    }
+  if$
+}
+EOD
+  	}
+	$found{formatdate} = 1;
+    }
+
+    # If the style file didn't supply a format.title function, then supply
+    # one here (the {webpage} function requires it).
+    if (! $found{formattitle}) {
+	print OUT <<'EOD';
+FUNCTION {format.title}
+{ title empty$
+    { "" }
+    { title "t" change.case$ }
+  if$
+}
+EOD
+    $found{formattitle} = 1;
+    }
+}
+
+# Utility function: Keep track of open and close braces in the string argument.
+# Keep state in $bracematchtotal, return the current value.
+sub bracematcher {
+    my $s = shift;
+    $s =~ s/[^\{\}]//g;
+    #print "s=$s\n";
+    foreach my $c (split (//, $s)) {
+	$bracematchtotal += ($c eq '{' ? 1 : -1);
+    }
+    return $bracematchtotal;
+}
+
+# Utility function: use bracematcher to copy the complete block which starts
+# on or after the current line.
+sub copy_block {
+    $bracematchtotal = 0;
+    # copy any leading lines which don't have braces (presumably comments)
+    while (defined ($line = <IN>) && ($line !~ /{/)) {
+        print OUT $line;
+    }
+    while (defined ($line) && bracematcher($line) > 0) {
+        print OUT $line;
+        $line = <IN>;
+    }
+    print OUT "$line\n";	# print out terminating \} (assumed
+    				# alone on the line)
+}

thesis_template/PhDtemplateLATEX/Latex/Macros/MacroFile1.tex

@@ -0,0 +1,73 @@
+% This file contains macros that can be called up from connected TeX files
+% It helps to summarise repeated code, e.g. figure insertion (see below).
+
+% insert a centered figure with caption and description
+% parameters 1:filename, 2:title, 3:description and label
+\newcommand{\figuremacro}[3]{
+	\begin{figure}[htbp]
+		\centering
+		\includegraphics[width=1\textwidth]{#1}
+		\caption[#2]{\textbf{#2} - #3}
+		\label{#1}
+	\end{figure}
+}
+
+% insert a centered figure with caption and description AND WIDTH
+% parameters 1:filename, 2:title, 3:description and label, 4: textwidth
+% textwidth 1 means as text, 0.5 means half the width of the text
+\newcommand{\figuremacroW}[4]{
+	\begin{figure}[htbp]
+		\centering
+		\includegraphics[width=#4\textwidth]{#1}
+		\caption[#2]{\textbf{#2} - #3}
+		\label{#1}
+	\end{figure}
+}
+
+% inserts a figure with wrapped around text; only suitable for NARROW figs
+% o is for outside on a double paged document; others: l, r, i(inside)
+% text and figure will each be half of the document width
+% note: long captions often crash with adjacent content; take care
+% in general: above 2 macro produce more reliable layout
+\newcommand{\figuremacroN}[3]{
+	\begin{wrapfigure}{o}{0.5\textwidth}
+		\centering
+		\includegraphics[width=0.48\textwidth]{#1}
+		\caption[#2]{{\small\textbf{#2} - #3}}
+		\label{#1}
+	\end{wrapfigure}
+}
+
+% predefined commands by Harish
+\newcommand{\PdfPsText}[2]{
+  \ifpdf
+     #1
+  \else
+     #2
+  \fi
+}
+
+\newcommand{\IncludeGraphicsH}[3]{
+  \PdfPsText{\includegraphics[height=#2]{#1}}{\includegraphics[bb = #3, height=#2]{#1}}
+}
+
+\newcommand{\IncludeGraphicsW}[3]{
+  \PdfPsText{\includegraphics[width=#2]{#1}}{\includegraphics[bb = #3, width=#2]{#1}}
+}
+
+\newcommand{\InsertFig}[3]{
+  \begin{figure}[!htbp]
+    \begin{center}
+      \leavevmode
+      #1
+      \caption{#2}
+      \label{#3}
+    \end{center}
+  \end{figure}
+}
+
+
+%%% Local Variables: 
+%%% mode: latex
+%%% TeX-master: "~/Documents/LaTeX/CUEDThesisPSnPDF/thesis"
+%%% End: 

thesis_template/PhDtemplateLATEX/Latex/StyleFiles/watermark.sty

@@ -0,0 +1,87 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{watermark}
+         [2002/01/29 v1.00 Watermarks (NCC)]
+%
+% The package provides watermarks on output pages. A watermark is
+% some text or picture printed at the background of paper. A watermark
+% is prepared in picture box stored at the beginning of running head.
+% So, the watermark material must be put on the page with LaTeX's \put and
+% \multiput commands.
+%
+% \watermark{BODY}      sets a watermark to be printed on all pages
+% \leftwatermark{BODY}  sets a watermark to be printed on every even page
+%                       if twoside mode is turned on. Otherwise, this
+%                       watermark is ignored. Odd-page watermark
+%                       leaves unchanged.
+% \rightwatermark{BODY} sets a watermark to be printed on every odd page
+%                       if twoside mode is turned on. Otherwise, this
+%                       watermark is printed on all pages. Even-page
+%                       watermark leaves unchanged.
+% \thiswatermark{BODY}  sets a watermark for the current page only.
+%
+% Additionally, the package provides the command \thispageheading{HEADING}
+% which replaces a heading for the current page to specified heading.
+% Watermarks are also printed when a heading is replaced.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% We use the \@begindvi hook from the output routine.
+% This hook works only once at the beginning of dvi, but some packages
+% (e.g. hyperref) also use it for their own needs.
+% So, we redefine it at the beginning of document in such a way to 
+% accurately save its behaviour after the first call when it can be
+% redefined by other packages.
+%
+\AtBeginDocument{
+  \let\WMK@begindvi\@begindvi
+  \def\@begindvi{\WMK@begindvi \WMK@insert
+    \global\let\WMK@begindvi\@begindvi       % Save redefined behaviour and
+    \gdef\@begindvi{\WMK@begindvi\WMK@insert}% redefine \@begindvi once more
+  }%
+}
+%
+% The \WMK@insert command redefines current header and inserts the
+% \WMK@hook at the beginning of header. A box produced by this hook
+% has zero natural sizes.
+%
+\def\WMK@insert{\let\WMK@head\@thehead \def\@thehead{\WMK@hook\WMK@head}}
+\def\WMK@hook{%
+  \begin{picture}(0,0)\relax
+    \ifx\WMK@this\relax
+      \if@twoside
+        \ifodd\c@page\WMK@odd\else\WMK@even\fi
+      \else
+        \WMK@odd
+      \fi
+    \else
+      \WMK@this \global\let\WMK@this\relax
+    \fi
+  \end{picture}%
+}
+%
+% Define watermark producing commands
+%
+\newcommand{\watermark}[1]{\leftwatermark{#1}\rightwatermark{#1}}
+\newcommand{\leftwatermark}[1]{\long\gdef\WMK@even{#1}}
+\newcommand{\rightwatermark}[1]{\long\gdef\WMK@odd{#1}}
+\newcommand{\thiswatermark}[1]{\long\gdef\WMK@this{#1}}
+\watermark{}
+\let\WMK@this\relax
+%
+% Now we define \thispageheading{heading} command.
+% It replaces a heading on the current page to the
+% specified one and prepares it in \parbox. Watermarks are leaved unchanged.
+% The \ifWMK@savehead is needed to protect from multiple use of this command
+% on the same page.
+%
+\newif\ifWMK@savehead \WMK@saveheadfalse
+\newcommand{\thispageheading}[1]{%
+  \ifWMK@savehead \else
+    \global\WMK@saveheadtrue \global\let\WMK@savehook\WMK@hook
+  \fi
+  \long\gdef\WMK@hook{\WMK@savehook
+    \parbox[t]\textwidth{#1}\let\WMK@head\@empty
+    \global\WMK@saveheadfalse \global\let\WMK@hook\WMK@savehook
+  }%
+}
+\endinput

thesis_template/PhDtemplateLATEX/thesis.brf

@@ -0,0 +1,3 @@
+\backcite {lastname07}{{1}{1.1.1}{subsection.1.1.1}}
+\backcite {lastname07}{{1}{1.1.1}{subsection.1.1.1}}
+\backcite {name06}{{1}{1.1.1}{subsection.1.1.1}}

thesis_template/PhDtemplateLATEX/thesis.nlo

@@ -0,0 +1,4 @@
+\nomenclatureentry{aDAPI@[{DAPI}]\begingroup 4',6-diamidino-2-phenylindole; a fluorescent stain that binds strongly to DNA and serves to marks the nucleus in fluorescence microscopy\nomeqref {0}|nompageref}{viii}
+\nomenclatureentry{aDEPC@[{DEPC}]\begingroup diethyl-pyro-carbonate; used to remove RNA-degrading enzymes (RNAases) from water and laboratory utensils\nomeqref {0}|nompageref}{viii}
+\nomenclatureentry{aDMSO@[{DMSO}]\begingroup dimethyl sulfoxide; organic solvent, readily passes through skin, cryoprotectant in cell culture\nomeqref {0}|nompageref}{viii}
+\nomenclatureentry{aEDTA@[{EDTA}]\begingroup Ethylene-diamine-tetraacetic acid; a chelating (two-pronged) molecule used to sequester most divalent (or trivalent) metal ions, such as calcium (Ca$^{2+}$) and magnesium (Mg$^{2+}$), copper (Cu$^{2+}$), or iron (Fe$^{2+}$ / Fe$^{3+}$)\nomeqref {0}|nompageref}{viii}

thesis_template/PhDtemplateLATEX/thesis.nls

@@ -0,0 +1,14 @@
+\begin{thenomenclature} 
+
+ \nomgroup{A}
+
+  \item [{DAPI}]\begingroup 4',6-diamidino-2-phenylindole; a fluorescent stain that binds strongly to DNA and serves to marks the nucleus in fluorescence microscopy\nomeqref {0}
+		\nompageref{viii}
+  \item [{DEPC}]\begingroup diethyl-pyro-carbonate; used to remove RNA-degrading enzymes (RNAases) from water and laboratory utensils\nomeqref {0}
+		\nompageref{viii}
+  \item [{DMSO}]\begingroup dimethyl sulfoxide; organic solvent, readily passes through skin, cryoprotectant in cell culture\nomeqref {0}
+		\nompageref{viii}
+  \item [{EDTA}]\begingroup Ethylene-diamine-tetraacetic acid; a chelating (two-pronged) molecule used to sequester most divalent (or trivalent) metal ions, such as calcium (Ca$^{2+}$) and magnesium (Mg$^{2+}$), copper (Cu$^{2+}$), or iron (Fe$^{2+}$ / Fe$^{3+}$)\nomeqref {0}
+		\nompageref{viii}
+
+\end{thenomenclature}

thesis_template/PhDtemplateLATEX/thesis.out

@@ -0,0 +1,12 @@
+\BOOKMARK [0][]{section*.3}{List of Figures}{}
+\BOOKMARK [0][]{section*.5}{List of Tables}{}
+\BOOKMARK [0][]{chapter*.6}{Glossary}{}
+\BOOKMARK [0][]{chapter.1}{1 Introduction}{}
+\BOOKMARK [1][]{section.1.1}{1.1 put section name here}{chapter.1}
+\BOOKMARK [2][]{subsection.1.1.1}{1.1.1 Name your subsection}{section.1.1}
+\BOOKMARK [0][]{chapter.2}{2 Aims of the project}{}
+\BOOKMARK [1][]{section.2.1}{2.1 Final aim}{chapter.2}
+\BOOKMARK [1][]{section.2.2}{2.2 Preliminary aims}{chapter.2}
+\BOOKMARK [0][]{chapter.3}{3 Discussion}{}
+\BOOKMARK [0][]{chapter.4}{4 Materials \046 methods}{}
+\BOOKMARK [0][]{section*.11}{References}{}

thesis_template/PhDtemplateLATEX/thesis.tex

@@ -0,0 +1,257 @@
+
+% ----------------------------------------------------------------------
+%                   LATEX TEMPLATE FOR PhD THESIS
+% ----------------------------------------------------------------------
+
+% based on Harish Bhanderi's PhD/MPhil template, then Uni Cambridge
+% http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/ThesisStyle/
+% corrected and extended in 2007 by Jakob Suckale, then MPI-CBG PhD programme
+% and made available through OpenWetWare.org - the free biology wiki
+
+
+%: Style file for Latex
+% Most style definitions are in the external file PhDthesisPSnPDF.
+% In this template package, it can be found in ./Latex/Classes/
+\documentclass[twoside,11pt]{Latex/Classes/PhDthesisPSnPDF}
+
+
+%: Macro file for Latex
+% Macros help you summarise frequently repeated Latex commands.
+% Here, they are placed in an external file /Latex/Macros/MacroFile1.tex
+% An macro that you may use frequently is the figuremacro (see introduction.tex)
+\include{Latex/Macros/MacroFile1}
+
+
+
+%: ----------------------------------------------------------------------
+%:                  TITLE PAGE: name, degree,..
+% ----------------------------------------------------------------------
+% below is to generate the title page with crest and author name
+
+%if output to PDF then put the following in PDF header
+\ifpdf  
+    \pdfinfo { /Title  (PhD and MPhil Thesis Classes)
+               /Creator (TeX)
+               /Producer (pdfTeX)
+               /Author (YourName your@email.net)
+               /CreationDate (D:YYYYMMDDhhmmss)  %format D:YYYYMMDDhhmmss
+               /ModDate (D:YYYYMMDDhhmm)
+               /Subject (xyz)
+               /Keywords (add, your, keywords, here) }
+    \pdfcatalog { /PageMode (/UseOutlines)
+                  /OpenAction (fitbh)  }
+\fi
+
+
+\title{Title of your thesis}
+
+
+
+% ----------------------------------------------------------------------
+% The section below defines www links/email for author and institutions
+% They will appear on the title page of the PDF and can be clicked
+\ifpdf
+  \author{\href{mailto:your@email.net}{YourName}}
+%  \cityofbirth{born in XYZ} % uncomment this if your university requires this
+%  % If city of birth is required, also uncomment 2 sections in PhDthesisPSnPDF
+%  % Just search for the "city" and you'll find them.
+  \collegeordept{\href{http://www.something.net}{CollegeOrDepartment}}
+  \university{\href{http://www.something.net}{University}}
+
+  % The crest is a graphics file of the logo of your research institution.
+  % Place it in ./0_frontmatter/figures and specify the width
+  \crest{\includegraphics[width=4cm]{logo}}
+  
+% If you are not creating a PDF then use the following. The default is PDF.
+\else
+  \author{YourName}
+%  \cityofbirth{born in XYZ}
+  \collegeordept{CollegeOrDept}
+  \university{University}
+  \crest{\includegraphics[width=4cm]{logo}}
+\fi
+
+%\renewcommand{\submittedtext}{change the default text here if needed}
+\degree{Philosophi\ae Doctor (PhD), DPhil,..}
+\degreedate{year month}
+
+
+% ----------------------------------------------------------------------
+       
+% turn of those nasty overfull and underfull hboxes
+\hbadness=10000
+\hfuzz=50pt
+
+
+%: --------------------------------------------------------------
+%:                  FRONT MATTER: dedications, abstract,..
+% --------------------------------------------------------------
+
+\begin{document}
+
+%\language{english}
+
+% sets line spacing
+\renewcommand\baselinestretch{1.2}
+\baselineskip=18pt plus1pt
+
+
+%: ----------------------- generate cover page ------------------------
+
+\maketitle  % command to print the title page with above variables
+
+
+%: ----------------------- cover page back side ------------------------
+% Your research institution may require reviewer names, etc.
+% This cover back side is required by Dresden Med Fac; uncomment if needed.
+
+\newpage
+\vspace{10mm}
+1. Reviewer: Name
+
+\vspace{10mm}
+2. Reviewer: 
+
+\vspace{20mm}
+Day of the defense:
+
+\vspace{20mm}
+\hspace{70mm}Signature from head of PhD committee:
+
+
+
+%: ----------------------- abstract ------------------------
+
+% Your institution may have specific regulations if you need an abstract and where it is to be placed in the document. The default here is just after title.
+
+\include{0_frontmatter/abstract}
+
+% The original template provides and abstractseparate environment, if your institution requires them to be separate. I think it's easier to print the abstract from the complete thesis by restricting printing to the relevant page.
+% \begin{abstractseparate}
+%   \input{Abstract/abstract}
+% \end{abstractseparate}
+
+
+%: ----------------------- tie in front matter ------------------------
+
+\frontmatter
+\include{0_frontmatter/dedication}
+\include{0_frontmatter/acknowledgement}
+
+
+%: ----------------------- contents ------------------------
+
+\setcounter{secnumdepth}{3} % organisational level that receives a numbers
+\setcounter{tocdepth}{3}    % print table of contents for level 3
+\tableofcontents            % print the table of contents
+% levels are: 0 - chapter, 1 - section, 2 - subsection, 3 - subsection
+
+
+%: ----------------------- list of figures/tables ------------------------
+
+\listoffigures	% print list of figures
+
+\listoftables  % print list of tables
+
+
+%: ----------------------- glossary ------------------------
+
+% Tie in external source file for definitions: /0_frontmatter/glossary.tex
+% Glossary entries can also be defined in the main text. See glossary.tex
+\include{0_frontmatter/glossary} 
+
+\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]
+\begin{footnotesize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)
+
+\printnomenclature[1.5cm] % [] = distance between entry and description
+\label{nom} % target name for links to glossary
+
+\end{footnotesize}
+\end{multicols}
+
+
+
+%: --------------------------------------------------------------
+%:                  MAIN DOCUMENT SECTION
+% --------------------------------------------------------------
+
+% the main text starts here with the introduction, 1st chapter,...
+\mainmatter
+
+\renewcommand{\chaptername}{} % uncomment to print only "1" not "Chapter 1"
+
+
+%: ----------------------- subdocuments ------------------------
+
+% Parts of the thesis are included below. Rename the files as required.
+% But take care that the paths match. You can also change the order of appearance by moving the include commands.
+
+\include{1_introduction/introduction}	% background information
+\include{2/aims}						% aims of the project
+
+\include{3/XYZ}			
+\include{4/XYZ}	
+\include{5/XYZ}
+\include{6/XYZ}
+
+\include{7/discussion}               % discussion of results
+
+\include{8/materials_methods}        % description of lab methods
+
+
+
+
+% --------------------------------------------------------------
+%:                  BACK MATTER: appendices, refs,..
+% --------------------------------------------------------------
+
+% the back matter: appendix and references close the thesis
+
+
+%: ----------------------- bibliography ------------------------
+
+% The section below defines how references are listed and formatted
+% The default below is 2 columns, small font, complete author names.
+% Entries are also linked back to the page number in the text and to external URL if provided in the BibTex file.
+
+% PhDbiblio-url2 = names small caps, title bold & hyperlinked, link to page 
+\begin{multicols}{2} % \begin{multicols}{ # columns}[ header text][ space]
+\begin{tiny} % tiny(5) < scriptsize(7) < footnotesize(8) < small (9)
+
+\bibliographystyle{Latex/Classes/PhDbiblio-url2} % Title is link if provided
+\renewcommand{\bibname}{References} % changes the header; default: Bibliography
+
+\bibliography{9_backmatter/references} % adjust this to fit your BibTex file
+
+\end{tiny}
+\end{multicols}
+
+% --------------------------------------------------------------
+% Various bibliography styles exit. Replace above style as desired.
+
+% in-text refs: (1) (1; 2)
+% ref list: alphabetical; author(s) in small caps; initials last name; page(s)
+%\bibliographystyle{Latex/Classes/PhDbiblio-case} % title forced lower case
+%\bibliographystyle{Latex/Classes/PhDbiblio-bold} % title as in bibtex but bold
+%\bibliographystyle{Latex/Classes/PhDbiblio-url} % bold + www link if provided
+
+%\bibliographystyle{Latex/Classes/jmb} % calls style file jmb.bst
+% in-text refs: author (year) without brackets
+% ref list: alphabetical; author(s) in normal font; last name, initials; page(s)
+
+%\bibliographystyle{plainnat} % calls style file plainnat.bst
+% in-text refs: author (year) without brackets
+% (this works with package natbib)
+
+
+% --------------------------------------------------------------
+
+% according to Dresden med fac summary has to be at the end
+%\include{0_frontmatter/abstract}
+
+%: Declaration of originality
+\include{9_backmatter/declaration}
+
+
+
+\end{document}