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tex-files/abbreviations.tex 0 → 100644
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\addcontentsline{toc}{chapter}{List of Abbreviations}
\chapter*{List of Abbreviations}
DNCB : 2,4-Dinitrochlorobenzene \\
DPCP : Diphenylcyclopropenone \\
HaCaT : Keratinocyte cell line \\
LC : Liquid Chromatography \\
MS : Mass Spectrometry \\
MS/MS : Tandem mass spectrometry
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tex-files/abstract.tex 0 → 100644
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\addcontentsline{toc}{chapter}{Abstract}
\chapter*{Abstract}
This files is where I write the abstract in tex for the front matter
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tex-files/acknowledgements.tex 0 → 100644
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\addcontentsline{toc}{chapter}{Acknowledgements}
\chapter*{Acknowledgements}
I would like to thank my Teddy and Terry for distracting me in the production
of this thesis dissertation.
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tex-files/declaration.tex 0 → 100644
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\addcontentsline{toc}{chapter}{Declaration}
\chapter*{Declaration}
I, Monika Kudelska
declare that the thesis entitled:
My awesome project % Change to dissertation title
and the work presented in it are my own and has been generated by me as the result of my own original research.
I confirm that:
\begin{enumerate}
\item This work was done wholly or mainly while in candidature for a research degree at this University;
\item Where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated;
\item Where I have consulted the published work of others, this is always clearly attributed;
\item Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work;
\item I have acknowledged all main sources of help;
\item Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself;
\item None of this work has been published before submission.
\end{enumerate}
Signed:
Date:
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tex-files/mkthesis.sty 0 → 100644
View file @ 1d941448
\pagestyle{empty}
\setlength{\parskip}{2ex plus 0.5ex minus 0.2ex}
\setlength{\parindent}{0pt}
\makeatletter %to avoid error messages generated by "\@". Makes Latex treat "@" like a letter
%29. The Title page (of every volume if more than one) must contain the following information in the order shown
% University of Southampton[1]
% Name of the Faculty and Faculty in which the research was conducted
% Full title of the thesis and any subtitle
% Total number of volumes (if more than one) and the number of that particular volume
% Your full name followed, if you wish, by any qualifications and distinctions
% Qualification for which the thesis is submitted
% Month and year of submission
\linespread{1.5}
\def\submitdate#1{\gdef\@submitdate{#1}}
\submitdate{\today} % Submission date supplied in 00-preface.Rmd
\def\maketitle{
\begin{titlepage}{
%\linespread{1.5}
\Large School of Biological Sciences \\
University of Southampton
\rm
\vskip 3in
\Large \bf
\@title \par % Title supplied in 00-preface.Rmd
}
\vskip 0.3in
\par
{\Large \@author} % Author name supplied in 00-preface.Rmd
\vskip 4in
\par
Submitted in part fulfilment of the requirements for the degree of
\linebreak
Doctor of Philosophy at the University of Southampton, \@submitdate
\vfil
\end{titlepage}
}
\def\titlepage{
\newpage
\centering
\linespread{1}
\normalsize
\vbox to \vsize\bgroup\vbox to 9in\bgroup
}
\def\endtitlepage{
\par
\kern 0pt
\egroup
\vss
\egroup
\cleardoublepage
}
% Preface with Roman numbering reading the files kept in tex-files folder
% The order of the preface is currently: Abstract, Table of Contents, List of Tables,
% List of Figures, List of Abbreviations, Declaration, Acknowledgments
\def\preface{
\pagenumbering{roman}
\pagestyle{plain}
\doublespacing
% Abstract
\phantomsection
\input{tex-files/abstract.tex}
\cleardoublepage
%Table of contents
\phantomsection
\pdfbookmark[0]{\contentsname}{toc}
\tableofcontents
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
% List of tables
\phantomsection
\listoftables
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
% List of Figures
\phantomsection
\listoffigures
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
% Abbreviations
\phantomsection
\input{tex-files/abbreviations.tex}
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
% Declaration of Authorship
\phantomsection
\input{tex-files/declaration.tex}
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
% Acknowledgements
\phantomsection
\input{tex-files/acknowledgements.tex}
\pagestyle{plain}
\cleardoublepage
\pagestyle{uheadings}
}
% Now change the stlye for the body and use underlined pages with Arabic Numbering
\def\body{
\pagestyle{uheadings}
\pagenumbering{arabic}
\doublespacing
}
\makeatother %to avoid error messages generated by "\@". Makes Latex treat "@" like a letter
\setlength{\parskip}{\medskipamount} % a little space before a \par
\setlength{\parindent}{0pt} % don't indent first lines of paragraphs
tex-files/preamble.tex 0 → 100644
View file @ 1d941448
% Peamble - load all the packages
\usepackage[none]{hyphenat}
\usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs
\usepackage[default,osfigures,scale=0.95]{opensans} % Open sans font
\usepackage{lmodern}
\usepackage{lettrine} % The lettrine is the first enlarged letter at the beginning of the text
\usepackage{appendix}
\usepackage{graphicx}
\usepackage{lscape}
\usepackage{pdfpages} % include pdf pages
\usepackage{microtype} % Try to prevent badbox errors
\usepackage{float}
\usepackage{wrapfig}
\usepackage{verbatim}
\usepackage{amssymb}
\usepackage{wasysym}
\usepackage{fixltx2e}
\usepackage{subfig}
\usepackage{mathpazo,mathrsfs}
\usepackage{latexsym}
\usepackage{sidecap}
\usepackage{eucal}
\usepackage{setspace}
\usepackage{ragged2e}
%\raggedbottom
\usepackage{makeidx} % These lines add bibliography to TOC
\makeindex
\usepackage[nottoc]{tocbibind}
\usepackage{natbib}
\setcitestyle{authoryear,aysep={,}} % needed to fully emulate harvard's "dcu" citation style
\usepackage{har2nat}
\renewcommand{\bibname}{References} % Rename biblography as References
\usepackage{bookmark}
% Read in the style files for the
\input{tex-files/uhead.sty} % underlined header for pages
\input{tex-files/mkthesis.sty} % Defines the front matter and other bits and pieces
tex-files/uhead.sty 0 → 100644
View file @ 1d941448
%UHEAD.STY If this is included after \documentstyle{report}, it adds
% an underlined heading style to the LaTeX report style.
% \pagestyle{uheadings} will put underlined headings at the top
% of each page. The right page headings are the Chapter titles and
% the left page titles are supplied by \def\lefthead{text}.
% Ted Shapin, Dec. 17, 1986
\makeatletter
\def\chapapp2{Chapter}
\def\appendix{\par
\setcounter{chapter}{0}
\setcounter{section}{0}
\def\chapapp2{Appendix}
\def\@chapapp{Appendix}
\def\thechapter{\Alph{chapter}}}
\def\ps@uheadings{\let\@mkboth\markboth
% modifications
% Commented out the oddhead and copied evenhead to remove section heads
% A. Bailey Dec. 9th 2012
%\def\@oddhead{\protect\underline{\protect\makebox[\textwidth][l]
% {\sl\rightmark\hfill\rm\thepage}}}
\def\@oddhead{\protect\underline{\protect\makebox[\textwidth][l]
{\rm\hfill\sl\leftmark}}}
%\def\@oddfoot{\thepage}
%\def\@evenfoot{\thepage}
\def\@evenhead{\protect\underline{\protect\makebox[\textwidth][l]
{\rm\hfill\sl\leftmark}}}
% end of modifications
\def\chaptermark##1{\markboth {\ifnum \c@secnumdepth >\m@ne
\chapapp2\ \thechapter. \ \fi ##1}{}}%
\def\sectionmark##1{\markright {\ifnum \c@secnumdepth >\z@
\thesection. \ \fi ##1}}}
\makeatother
thesis-template.Rproj 0 → 100644
View file @ 1d941448
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: knitr
LaTeX: pdfLaTeX
BuildType: Website
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