ADD outline tex file

.gitignore

@@ -4,9 +4,9 @@
 !*.bbl
 !*.glo
 
-!src
-src/*
-!src/*.tex
-!src/*.bib
-!src/*.bbl
-!src/*.glo
+!tex
+tex/*
+!tex/*.tex
+!tex/*.bib
+!tex/*.bbl
+!tex/*.glo

tex/thesis.tex

@@ -0,0 +1,227 @@
+\documentclass[twocolumn]{article}
+\usepackage[top=0.75in,left=0.75in,right=0.75in,bottom=0.9in]{geometry}
+\usepackage{siunitx}
+\usepackage[acronym]{glossaries}
+\usepackage[T1]{fontenc}
+\usepackage{enumitem}
+\usepackage{titlesec}
+\usepackage{titlecaps}
+\usepackage{upgreek}
+\usepackage{graphicx}
+\usepackage{subcaption}
+\usepackage{nth}
+\usepackage[capitalize]{cleveref}
+\usepackage[version=4]{mhchem}
+\usepackage{pgfgantt}
+
+\titleformat{\section}[block]{\bfseries\large}{}{0pt}{\uppercase}
+\titleformat{\subsection}[block]{\bfseries\large}{}{0pt}{\titlecap}
+\titleformat{\subsubsection}[block]{\itshape\large}{}{0pt}{\titlecap}
+\titleformat{\paragraph}[runin]{\bfseries\itshape}{}{0pt}{\titlecap}
+
+\setlist[description]{font=$\bullet$~\textbf\normalfont}
+
+\sisetup{per-mode=symbol,list-units=single}
+\DeclareSIUnit\activityunit{U}
+\DeclareSIUnit\carrier{carriers}
+\DeclareSIUnit\cell{cells}
+\DeclareSIUnit\ab{mAbs}
+\DeclareSIUnit\molar{M}
+\DeclareSIUnit\gforce{\times{} g}
+
+% add acronyms here
+\renewcommand{\glossarysection}[2][]{} % remove glossary title
+\makeglossaries
+\newacronym{act}{ACT}{adoptive cell therapies}
+
+\begin{document}
+
+\begin{titlepage}
+  \begin{center}
+
+    \huge\textbf{Optimizing T Cell Manufacturing and Quality Using
+      Functionalized Degradable Microscaffolds}
+
+    \vfill
+
+    \LARGE Nathan John Dwarshuis, B.S. \\
+
+    \vspace{1.5em}
+
+    \Large PhD Thesis \\
+    Doctor of Philosophy in Biomedical Engineering \\
+    Georgia Institute of Technology and Emory University
+
+    \vspace{1.5em}
+
+    \large\today
+
+    \vfill
+
+  \end{center}
+
+  \large{
+
+  \noindent
+  Committee Members
+
+  \vspace{1.5em}
+  
+  \noindent
+  Dr. Krishnendu Roy (Advisor) \\
+  Wallace H. Coulter Department of Biomedical Engineering, Georgia
+  Institute of Technology and Emory University
+
+  \vspace{1.5em}
+
+  \noindent
+  Dr. Madhav Dhodapkar \\
+  Department of Hematology and Medical Oncology, Emory University
+
+  \vspace{1.5em}
+
+  \noindent
+  Dr. Melissa Kemp \\
+  Wallace H. Coulter Department of Biomedical Engineering, Georgia
+  Institute of Technology and Emory University
+
+  \vspace{1.5em}
+
+  \noindent
+  Dr. Wilbur Lam \\
+  Wallace H. Coulter Department of Biomedical Engineering, Georgia
+  Institute of Technology and Emory University
+
+  \vspace{1.5em}
+
+  \noindent
+  Dr. Sakis Mantalaris \\
+  Wallace H. Coulter Department of Biomedical Engineering, Georgia
+  Institute of Technology and Emory University }
+\end{titlepage}
+
+\onecolumn \pagenumbering{roman}
+\clearpage
+
+% TODO
+Insert witty quote here
+
+\clearpage
+
+\section*{acknowledgements}
+
+Thank you to Lex Fridman and Devin Townsend for being awesome and inspirational.
+
+\clearpage
+
+\section*{abstract}
+
+Insert abstract here.
+
+\clearpage
+
+\tableofcontents
+
+\clearpage
+
+\listoffigures
+
+\clearpage
+
+\listoftables
+
+\clearpage
+
+\twocolumn
+\section*{acronyms}
+
+\printglossary[type=\acronymtype]
+
+\clearpage
+\pagenumbering{arabic}
+
+\clearpage
+
+\section{introduction}
+
+\subsection*{overview}
+
+Insert overview here
+
+\subsection*{hypothesis}
+
+Insert hypothesis here
+
+\subsection*{specific aims}
+\subsubsection*{aim 1}
+\subsubsection*{aim 2}
+\subsubsection*{aim 3}
+
+\subsection*{outline}
+
+\subsubsection*{Aim 1}
+
+Aim 1
+
+\subsubsection*{Aim 2}
+
+Aim 2
+
+\subsubsection*{Aim 3}
+
+Aim 3
+
+\section{background and significance}
+\subsubsection*{background}
+\subsubsection*{current T cell manufacturing technologies}
+
+bla bla
+
+\subsection*{strategies to optimize cell manufacturing}
+
+bla bla
+
+\subsubsection*{strategies to characterize cell manufacturing}
+
+bla bla
+
+\subsection{Innovation}
+
+\section{aim 1}
+
+\subsection{introduction}
+\subsection{methods}
+\subsection{results}
+\subsection{discussion}
+
+\section{Aim 2}
+
+\subsection{introduction}
+\subsection{methods}
+\subsection{results}
+\subsection{discussion}
+
+\section{Aim 3}
+
+\subsection{introduction}
+\subsection{methods}
+\subsection{results}
+\subsection{discussion}
+
+\section{conclusions and future work}
+\subsection{conclusions}
+\subsection{future work}
+
+\onecolumn
+\clearpage
+
+% TODO some people put appendices here....not sure if I need to
+
+\section{References}
+\renewcommand{\section}[2]{} % noop the original bib section header
+
+\bibliography{../proposal}
+
+\bibliographystyle{naturemag}
+
+\end{document}