% -*- Mode:TeX -*-

%% IMPORTANT: The official thesis specifications are available at:
%%            http://libraries.mit.edu/archives/thesis-specs/
%%
%%            Please verify your thesis' formatting and copyright
%%            assignment before submission.  If you notice any
%%            discrepancies between these templates and the 
%%            MIT Libraries' specs, please let us know
%%            by e-mailing thesis@mit.edu

%% The documentclass options along with the pagestyle can be used to generate
%% a technical report, a draft copy, or a regular thesis.  You may need to
%% re-specify the pagestyle after you \include  cover.tex.  For more
%% information, see the first few lines of mitthesis.cls. 

%\documentclass[12pt,vi,twoside]{mitthesis}
%%
%%  If you want your thesis copyright to you instead of MIT, use the
%%  ``vi'' option, as above.
%%
%\documentclass[12pt,twoside,leftblank]{mitthesis}
%%
%% If you want blank pages before new chapters to be labelled ``This
%% Page Intentionally Left Blank'', use the ``leftblank'' option, as
%% above. 

\documentclass[12pt,twoside,singlespace]{mitthesis}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{hyperref}
\usepackage{natbib}
\usepackage{libertine}
\usepackage{inconsolata}

\renewcommand{\thesection}{\arabic{section}}

%%%%% better source code display
\usepackage{minted}

%% dyl fonts

% \usemintedstyle{friendly}
% \usemintedstyle{perldoc}
%\definecolor{bg}{rgb}{0.95,0.95,0.95}
\definecolor{bg}{rgb}{0.625,0,0}
\usemintedstyle{default}
\newcommand{\why}[1]{\\ \par{\footnotesize #1}}
%\setmonofont[Scale=0.9,BoldFont={Inconsolata Bold}]{Inconsolata}

%\usepackage[gray]{xcolor}
\newminted{clojure}{fontsize=\footnotesize}
%\newminted{clojure}{fontsize=\footnotesize,bgcolor=bg}
%\newminted{clojure}{fontsize=\scriptsize}

%\usepackage{lgrind}
\pagestyle{plain}

\begin{document}

\include{cover}
% Some departments (e.g. 5) require an additional signature page.  See
% signature.tex for more information and uncomment the following line if
% applicable.
% \include{signature}
\pagestyle{plain}
\tableofcontents
%\newpage
%\listoffigures
%\newpage
%\listoftables
\include{cortex}
\nocite{*}
%\include{chap2}
\appendix
\begin{singlespace}
\bibliography{cortex}
%\bibliographystyle{agsm}
%\bibliographystyle{apa}
\bibliographystyle{plainnat}
\end{singlespace}
\end{document}

