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genomics_course.tex
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Masters/Doctoral Thesis
% LaTeX Template
% Version 2.5 (27/8/17)
%
% This template was 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[
12pt, % 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
onehalfspacing, % Single line spacing, alternatives: singlespacing, 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{pdfpages}
\usepackage[T1]{fontenc} % Output font encoding for international characters
\usepackage{amsmath}
\usepackage{mathpazo} % Use the Palatino font by default
\usepackage{float}
\usepackage[backend=bibtex,style=numeric,sorting=none,natbib=true,backref=true,url=false]{biblatex} % Use the bibtex backend with the authoryear citation style (which resembles APA)
\usepackage{comment}
\usepackage{booktabs}
\usepackage[backref]{hyperref}
\addbibresource{final_bib.bib} % The filename of the bibliography
\usepackage[autostyle=true]{csquotes} % Required to generate language-dependent quotes in the bibliography
%\usepackage{caption}
%\captionsetup{font=small}
%----------------------------------------------------------------------------------------
% MARGIN SETTINGS
%----------------------------------------------------------------------------------------
\geometry{
paper=a4paper, % Change to letterpaper for US letter
inner=2.5cm, % Inner margin
outer=2.5cm, % Outer margin
bindingoffset=.5cm, % Binding offset
top=1.5cm, % Top margin
bottom=2cm, % Bottom margin
%showframe, % Uncomment to show how the type block is set on the page
}
%----------------------------------------------------------------------------------------
% THESIS INFORMATION
%----------------------------------------------------------------------------------------
\thesistitle{Introduction to Cancer genomics} % Your thesis title, this is used in the title and abstract, print it elsewhere with \ttitle
\supervisor{\hspace{-1cm} Dr. James \textsc{McKay}, Dr. Matthieu \textsc{Foll}} % 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, this is used in the title page and abstract, print it elsewhere with \degreename
\author{Aurélie \textsc{Gabriel}} % 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{Computational Biology} % Your subject area, this is not currently used anywhere in the template, print it elsewhere with \subjectname
\keywords{Omics data, Computational biology, Data integration, Lung cancer } % Keywords for your thesis, this is not currently used anywhere in the template, print it elsewhere with \keywordnames
\university{INSA de Lyon} % Your university's name and URL, this is used in the title page and abstract, print it elsewhere with \univname
\department{} % Your department's name and URL, this is used in the title page and abstract, print it elsewhere with \deptname
\group{Genetic Cancer Susceptibility group, IARC-WHO} % Your research group's name and URL, this is used in the title page, print it elsewhere with \groupname
\faculty{} % 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
}
%\usepackage{nomencl}
%\makenomenclature
%\renewcommand{\nomname}{Abbreviation list}
\usepackage[acronym]{glossaries}
\makeglossaries
%\setcounter{secnumdepth}{5}
\renewcommand*{\glstextformat}[1]{\textcolor{black}{#1}}
\include{acronyms}
\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
\mainmatter % Begin numeric (1,2,3...) page numbering
\pagestyle{thesis} % Return the page headers back to the "thesis" style
%----------------------------------------------------------------------------------------
% TITLE PAGE
%----------------------------------------------------------------------------------------
\begin{titlepage}
\begin{center}
\vspace*{.06\textheight}
%{\scshape\LARGE \univname\par}\vspace{1.5cm} % University name
\HRule \\[0.4cm] % Horizontal line
{\huge \bfseries \ttitle\par}\vspace{0.4cm} % thesis title
\HRule \\[1.5cm] % Horizontal line
\begin{flushright} \large
\emph{Author:}\\
\authorname % Author name - remove the \href bracket to remove the link
\end{flushright}
\vspace{3cm}
\vfill
\large \textit{This document comes from the first chapter of my PhD thesis, supervised by Dr. Matthieu Foll and Dr. James McKay and entitled "Integrating somatic and germline multi-omics data to improve our understanding of lung cancer: a computational biology perspective"}\\[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}
%----------------------------------------------------------------------------------------
% LIST OF CONTENTS/FIGURES/TABLES PAGES
%----------------------------------------------------------------------------------------
\tableofcontents % Prints the main table of contents
\listoftables % Prints the list of tables
\begingroup
\let\clearpage\relax
\listoffigures % Prints the list of figures
\endgroup
%----------------------------------------------------------------------------------------
% THESIS CONTENT - CHAPTERS
%----------------------------------------------------------------------------------------
%\mainmatter % Begin numeric (1,2,3...) page numbering
%\pagestyle{thesis} % Return the page headers back to the "thesis" style
%\begin{comment}
\include{Chapters/biology_introduction}
\include{Chapters/genomics_introduction}
\include{Chapters/lung_cancers}
\include{Chapters/method_introduction}
%----------------------------------------------------------------------------------------
% BIBLIOGRAPHY
%----------------------------------------------------------------------------------------
\printbibliography[heading=bibintoc]
%----------------------------------------------------------------------------------------
% ABBREVIATIONS
%----------------------------------------------------------------------------------------
%\printnomenclature
\newpage
\printglossaries
\addcontentsline{toc}{chapter}{Acronyms}
%\end{comment}
%----------------------------------------------------------------------------------------
\end{document}