%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is a template for LaTeX thesis (M.Sc. or PhD) at ZHAW.
%
% ZHAW thesis template downloaded from:
% https://github.com/matteodelucchi/ZHAW_thesis-template
%
% University specific changes were made by:
% Matteo Delucchi
%
% Based on a template downloaded from:
% http://www.LaTeXTemplates.com
%
% Version 2.x major modifications by:
% Vel (vel@latextemplates.com)
%
% This template is based on a template by:
% Steve Gunn (http://users.ecs.soton.ac.uk/srg/softwaretools/document/templates/)
% Sunil Patel (http://www.sunilpatel.co.uk/thesis-template/)
%
% Template license:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------------------------------------------------------------------------------
% PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
%----------------------------------------------------------------------------------------
\documentclass[
11pt, % The default document font size, options: 10pt, 11pt, 12pt
%oneside, % Two side (alternating margins) for binding by default, uncomment to switch to one side
english, % ngerman for German
singlespacing, % Single line spacing, alternatives: onehalfspacing or doublespacing
%draft, % Uncomment to enable draft mode (no pictures, no links, overfull hboxes indicated)
%nolistspacing, % If the document is onehalfspacing or doublespacing, uncomment this to set spacing in lists to single
%liststotoc, % Uncomment to add the list of figures/tables/etc to the table of contents
%toctotoc, % Uncomment to add the main table of contents to the table of contents
%parskip, % Uncomment to add space between paragraphs
%nohyperref, % Uncomment to not load the hyperref package
headsepline, % Uncomment to get a line under the header
%chapterinoneline, % Uncomment to place the chapter title next to the number on one line
%consistentlayout, % Uncomment to change the layout of the declaration, abstract and acknowledgements pages to match the default layout
]{MastersDoctoralThesis} % The class file specifying the document structure
\usepackage[utf8]{inputenc} % Required for inputting international characters
\usepackage[T1]{fontenc} % Output font encoding for international characters
\usepackage{xcolor}
%\usepackage[x-5pg]{pdfx} %for PDF-X support. Has problems with xcolor and hyperref
%\usepackage{subfigure}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{mathpazo} % Use the Palatino font by default
\usepackage[backend=biber, % Use the bibtex backend with the authoryear citation style (which resembles APA)
sorting=none, % numbers the reference in order of their appearance in the document. Troubleshoot with deleting all *.aux and *.bbl files and rebuild.
style=numeric-comp,
natbib=true]{biblatex}
\addbibresource{example.bib} % The filename of the bibliography
\usepackage[autostyle=true]{csquotes} % Required to generate language-dependent quotes in the bibliography
\usepackage{pdfpages}
\usepackage{todonotes}
\setlength{\marginparwidth}{2.5cm} % uncomment this if the todonotes are out of margins (cut off page)
\usepackage{listings}
\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codepurple}{rgb}{0.58,0,0.82}
\definecolor{backcolour}{rgb}{0.921, 0.929, 0.937} %0.95,0.95,0.92
\lstdefinestyle{mystyle}{
backgroundcolor=\color{backcolour},
commentstyle=\color{codegreen},
keywordstyle=\color{magenta},
numberstyle=\tiny\color{codegray},
stringstyle=\color{codepurple},
basicstyle=\ttfamily\footnotesize,
breakatwhitespace=false,
breaklines=true,
captionpos=b,
keepspaces=true,
numbers=left,
numbersep=5pt,
showspaces=false,
showstringspaces=false,
showtabs=false,
tabsize=2
}
\lstset{style=mystyle}
\usepackage{makecell} % formatting tables
%----------------------------------------------------------------------------------------
% MARGIN SETTINGS
%----------------------------------------------------------------------------------------
\geometry{
paper=a4paper, % Change to letterpaper for US letter
inner=2.5cm, % Inner margin
outer=3.8cm, % Outer margin
bindingoffset=.5cm, % Binding offset
top=1.5cm, % Top margin
bottom=1.5cm, % Bottom margin
%showframe, % Uncomment to show how the type block is set on the page
}
%----------------------------------------------------------------------------------------
% THESIS INFORMATION
%----------------------------------------------------------------------------------------
\thesistitle{Thesis Title} % Your thesis title, this is used in the title and abstract, print it elsewhere with \ttitle
\supervisor{Dr. James \textsc{Smith}} % Your supervisor's name, this is used in the title page, print it elsewhere with \supname
\examiner{} % Your examiner's name, this is not currently used anywhere in the template, print it elsewhere with \examname
\degree{Doctor of Philosophy} % Your degree name (Doctor of Philosophy or Master of Science), this is used in the title page and abstract, print it elsewhere with \degreename
\author{John \textsc{Smith}} % Your name, this is used in the title page and abstract, print it elsewhere with \authorname
\addresses{} % Your address, this is not currently used anywhere in the template, print it elsewhere with \addressname
\subject{Biological Sciences} % Your subject area, this is not currently used anywhere in the template, print it elsewhere with \subjectname
\keywords{} % Keywords for your thesis, this is not currently used anywhere in the template, print it elsewhere with \keywordnames
\university{\href{https://www.zhaw.ch/en/university/}{Zurich University of Applied Sciences}} % Your university's name and URL, this is used in the title page and abstract, print it elsewhere with \univname
\universitygerman{\href{https://www.zhaw.ch/de/hochschule/}{Z{\"u}rcher Hochschule f{\"u}r Angewandte Wissenschaften}}% Your university's name in german and URL, this is used in the german abstract (Zusammenfassung), print it elsewhere with \univnameger
\department{\href{https://www.zhaw.ch/en/lsfm/institutes-centres/ias/}{Institute of Applied Simulation}} % Your department's name and URL, this is used in the title page and abstract, print it elsewhere with \deptname
\group{\href{https://www.zhaw.ch/en/lsfm/institutes-centres/ias/research-development/computational-genomics/}{Applied Computational Genomics}} % Your research group's name and URL, this is used in the title page, print it elsewhere with \groupname
\faculty{\href{https://www.zhaw.ch/de/lsfm/}{Life Sciences and Facility Management
}} % Your faculty's name and URL, this is used in the title page and abstract, print it elsewhere with \facname
\AtBeginDocument{
\hypersetup{pdftitle=\ttitle} % Set the PDF's title to your title
\hypersetup{pdfauthor=\authorname} % Set the PDF's author to your name
\hypersetup{pdfkeywords=\keywordnames} % Set the PDF's keywords to your keywords
}
\begin{document}
\frontmatter % Use roman page numbering style (i, ii, iii, iv...) for the pre-content pages
\pagestyle{plain} % Default to the plain heading style until the thesis style is called for the body content
%----------------------------------------------------------------------------------------
% TITLE PAGE
%----------------------------------------------------------------------------------------
\begin{titlepage}
\begin{center}
\begin{figure}
\centering
\includegraphics[width=0.15\textwidth]{Figures/ZHAW_Logo.png} % Universtiy Logo, Adapted from: https://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/ZHAW_Logo.svg/879px-ZHAW_Logo.svg.png
\end{figure}
\vspace*{.06\textheight}
{\scshape\LARGE \univname\par}\vspace{1.5cm} % University name
\textsc{\Large Doctoral Thesis}\\[0.5cm] % Thesis type
\HRule \\[0.4cm] % Horizontal line
{\huge \bfseries \ttitle\par}\vspace{0.4cm} % Thesis title
\HRule \\[1.5cm] % Horizontal line
\begin{minipage}[t]{0.4\textwidth}
\begin{flushleft} \large
\emph{Author:}\\
\href{http://www.johnsmith.com}{\authorname} % Author name - remove the \href bracket to remove the link
\end{flushleft}
\end{minipage}
\begin{minipage}[t]{0.4\textwidth}
\begin{flushright} \large
\emph{Supervisor:} \\
\href{http://www.jamessmith.com}{\supname} % Supervisor name - remove the \href bracket to remove the link
\end{flushright}
\end{minipage}\\[3cm]
\vfill
\large \textit{A thesis submitted in fulfillment of the requirements\\ for the degree of \degreename}\\[0.3cm] % University requirement text
\textit{in the}\\[0.4cm]
\groupname\\\deptname\\[2cm] % Research group name and department name
\vfill
{\large \today}\\[4cm] % Date
%\includegraphics{Logo} % University/department logo - uncomment to place it
\vfill
\end{center}
\end{titlepage}
%----------------------------------------------------------------------------------------
% DECLARATION PAGE
%----------------------------------------------------------------------------------------
\begin{declaration}
\addchaptertocentry{\authorshipname} % Add the declaration to the table of contents
COMMENT THIS SECTION IF THE \href{https://www.zhaw.ch/en/lsfm/study/studiweb/master-ls/masters-thesis/}{ORIGINAL COPY OF THE ZHAW DECLARATION OF ORIGINALITY} IS USED IN THE APPENDIX.\newline
\noindent I, \authorname, declare that this thesis titled, \enquote{\ttitle} and the work presented in it are my own. I confirm that:
\begin{itemize}
\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.\\
\end{itemize}
\noindent Signed:\\
\rule[0.5em]{25em}{0.5pt} % This prints a line for the signature
\noindent Date:\\
\rule[0.5em]{25em}{0.5pt} % This prints a line to write the date
\end{declaration}
\cleardoublepage
%----------------------------------------------------------------------------------------
% QUOTATION PAGE
%----------------------------------------------------------------------------------------
\vspace*{0.2\textheight}
% \noindent\enquote{\itshape I'm fascinated by the idea that genetics is digital. A gene is a long sequence of coded letters, like computer information. Modern biology is becoming very much a branch of information technology.}\bigbreak
% \hfill Richard Dawkins
% \vspace*{0.2\textheight}
% \noindent\enquote{\itshape A line is a dot that went for a walk.}\bigbreak
% \hfill Paul Klee
\noindent\enquote{\itshape You can’t connect the dots looking forward; you can only connect them looking backwards. So you have to trust that the dots will somehow connect in your future. You have to trust in something – your gut, destiny, life, karma, whatever. Because believing that the dots will connect down the road will give you the confidence to follow your heart even when it leads you off the well worn path; and that will make all the difference.
}\bigbreak
\hfill{Steve Jobs} \newline
\strut\hfill{\tiny{(Stanford commencement speech, June 2005)}}
%----------------------------------------------------------------------------------------
% ABSTRACT PAGE
%----------------------------------------------------------------------------------------
\begin{abstract}
\addchaptertocentry{\abstractname} % Add the abstract to the table of contents
The Thesis Abstract is written here (and usually kept to just this page). The page is kept centered vertically so can expand into the blank space above the title too\ldots
Structure it the in the following way: context, Need (what we have), Need (what we want), task, object of the document, findings, Conclusion and perspectives.
\end{abstract}
%----------------------------------------------------------------------------------------
% German ABSTRACT PAGE
%----------------------------------------------------------------------------------------
\begin{extraAbstract}
\addchaptertocentry{\extraabstractname} % Add the abstract to the table of contents
Die Zusammenfassung der Dissertation wird hier geschrieben (und normalerweise nur auf dieser Seite gehalten). Die Seite wird vertikal zentriert, so dass sie sich auch in den leeren Raum über dem Titel ausdehnen kann\ldots
Strukturiere sie wie folgt: Kontext, Bedarf (was wir haben), Bedarf (was wir wollen), Aufgabe, Gegenstand des Dokuments, Ergebnisse, Schlussfolgerung und Perspektiven.
\end{extraAbstract}
%----------------------------------------------------------------------------------------
% ACKNOWLEDGEMENTS
%----------------------------------------------------------------------------------------
\begin{acknowledgements}
\addchaptertocentry{\acknowledgementname} % Add the acknowledgements to the table of contents
The acknowledgments and the people to thank go here, don't forget to include your project advisor\ldots
\end{acknowledgements}
%----------------------------------------------------------------------------------------
% LIST OF CONTENTS/FIGURES/TABLES PAGES
%----------------------------------------------------------------------------------------
\tableofcontents % Prints the main table of contents
\listoffigures % Prints the list of figures
\listoftables % Prints the list of tables
%----------------------------------------------------------------------------------------
% ABBREVIATIONS
%----------------------------------------------------------------------------------------
\begin{abbreviations}{ll} % Include a list of abbreviations (a table of two columns)
\textbf{LAH} & \textbf{L}ist \textbf{A}bbreviations \textbf{H}ere\\
\textbf{WSF} & \textbf{W}hat (it) \textbf{S}tands \textbf{F}or\\
\end{abbreviations}
%----------------------------------------------------------------------------------------
% PHYSICAL CONSTANTS/OTHER DEFINITIONS
%----------------------------------------------------------------------------------------
\begin{constants}{lr@{${}={}$}l} % The list of physical constants is a three column table
% The \SI{}{} command is provided by the siunitx package, see its documentation for instructions on how to use it
Speed of Light & $c_{0}$ & \SI{2.99792458e8}{\meter\per\second} (exact)\\
%Constant Name & $Symbol$ & $Constant Value$ with units\\
\end{constants}
%----------------------------------------------------------------------------------------
% SYMBOLS
%----------------------------------------------------------------------------------------
\begin{symbols}{lll} % Include a list of Symbols (a three column table)
$a$ & distance & \si{\meter} \\
$P$ & power & \si{\watt} (\si{\joule\per\second}) \\
%Symbol & Name & Unit \\
\addlinespace % Gap to separate the Roman symbols from the Greek
$\omega$ & angular frequency & \si{\radian} \\
\end{symbols}
%----------------------------------------------------------------------------------------
% DEDICATION
%----------------------------------------------------------------------------------------
\dedicatory{For/Dedicated to/To my\ldots}
%----------------------------------------------------------------------------------------
% PREFACE
%----------------------------------------------------------------------------------------
\begin{preface}
\addchaptertocentry{\prefacename} % Add the acknowledgements to the table of contents
Explain the motivation for the topic in general. Go through each chapter and explain how they contribute to your research question.
Check the thesis of Johannes John Carel Kuiper for a good example preface: \url{https://dspace.library.uu.nl/bitstream/handle/1874/90/full.pdf?sequence=2&isAllowed=y}
\end{preface}
%----------------------------------------------------------------------------------------
% THESIS CONTENT - CHAPTERS
%----------------------------------------------------------------------------------------
\mainmatter % Begin numeric (1,2,3...) page numbering
\pagestyle{thesis} % Return the page headers back to the "thesis" style
% Include the chapters of the thesis as separate files from the Chapters folder
% Uncomment the lines as you write the chapters
\include{Chapters/Chapter1}
%\include{Chapters/Chapter2}
%\include{Chapters/Chapter3}
%\include{Chapters/Chapter4}
%\include{Chapters/Chapter5}
%----------------------------------------------------------------------------------------
% THESIS CONTENT - APPENDICES
%----------------------------------------------------------------------------------------
\appendix % Cue to tell LaTeX that the following "chapters" are Appendices
% Include the appendices of the thesis as separate files from the Appendices folder
% Uncomment the lines as you write the Appendices
\include{Appendices/AppendixA}
\include{Appendices/DeclarationOfOriginalityZHAW} % from https://www.zhaw.ch/en/lsfm/study/studiweb/master-ls/masters-thesis/
%\include{Appendices/AppendixB}
%\include{Appendices/AppendixC}
%----------------------------------------------------------------------------------------
% BIBLIOGRAPHY
%----------------------------------------------------------------------------------------
\printbibliography[heading=bibintoc]
%----------------------------------------------------------------------------------------
\end{document}
