
% ----------------------------------------------------------------------
%                   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}
