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}