From 530339f9714c60bdf52a2e8b9bd2b8e39642e404 Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Mon, 2 Aug 2021 19:06:38 -0400
Subject: [PATCH] ADD appendix for the meta-analysis stuff

---
 tex/thesis.tex | 50 +++++++++++++++++++++++++++++++-------------------
 1 file changed, 31 insertions(+), 19 deletions(-)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index b7c9e5d..d70e7ee 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -14,6 +14,7 @@
 \usepackage{graphicx}
 \usepackage{subcaption}
 \usepackage{nth}
+\usepackage{hyperref} % must be before cleveref
 \usepackage[capitalize]{cleveref}
 \usepackage[version=4]{mhchem}
 \usepackage{pgfgantt}
@@ -160,6 +161,7 @@
 \newacronym{zfn}{ZFN}{zinc-finger nuclease}
 \newacronym{talen}{TALEN}{transcription activator-like effector nuclease}
 \newacronym{qbd}{QbD}{quality-by-design}
+\newacronym{aws}{AWS}{amazon web services}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % SI units for uber nerds
@@ -1583,18 +1585,6 @@ that were extrapolated from the standard curve were left unchanged.
 
 \subsection{data aggregation and meta-analysis}
 
-% TODO explain what the colors mean
-\begin{figure*}[ht!]
-  \begingroup
-
-  \includegraphics{../figures/metaanalysis.png}
-
-  \endgroup
-  \caption[Meta-analysis overview]
-  {Overview of strategy used for meta-analysis}
-  \label{fig:meta_overview}
-\end{figure*}
-
 In order to perform meta-analysis on all experimental data generate using the
 \gls{dms} system, we developed a program to curate and aggregate the raw
 datafiles into a \gls{sql} database (\cref{fig:meta_overview}).
@@ -1612,10 +1602,10 @@ experimental parameters such as the number of bead or \gls{dms} added.
 
 To aggregate the data in a database, we wrote a program using Python, R, and
 Docker which retrieved the data from its source location and inserted the data
-in a Postgres database. This program included checks to ensure the integrity of
-source data (for example, flagging entries which had a reagent whose
-manufacturing date was after the date the experiment started, which signifies a
-human input error).
+in a Postgres database (specifically Aurora implementation hosted on \gls{aws}).
+This program included checks to ensure the integrity of source data (for
+example, flagging entries which had a reagent whose manufacturing date was after
+the date the experiment started, which signifies a human input error).
 
 \subsection{statistical analysis}\label{sec:statistics}
 
@@ -4341,10 +4331,32 @@ expansion technology given that even in healthy donors, we observed the
 \onecolumn
 \clearpage
 
-% TODO some people put appendices here....not sure if I need to
+\appendix
+\chapter{meta analysis database code}\label{sec:appendix_meta}
 
-\chapter{References}
-\renewcommand{\section}[2]{} % noop the original bib section header
+The code used to aggregate all experimental data was written primarily in
+Python, with a subprocess running R in a Docker container to handle the flow
+cytometry data (\cref{fig:meta_overview}). The Postgres database itself was
+hosted using \gls{aws} using their proprietary Aurora implementation.
+
+% TODO explain what the colors mean
+\begin{figure*}[ht!]
+  \begingroup
+
+  \includegraphics{../figures/metaanalysis.png}
+
+  \endgroup
+  \caption[Meta-analysis overview]
+  {Overview of strategy used for meta-analysis}
+  \label{fig:meta_overview}
+\end{figure*}
+
+The code is available here: \url{https://github.gatech.edu/ndwarshuis3/mdma}.
+
+\chapter{reaction kinetics code}
+
+\chapter{references}
+\renewcommand{\chapter}[2]{} % noop the original bib section header
 
 \bibliography{references}