ADD appendix for the meta-analysis stuff

This commit is contained in:
Nathan Dwarshuis 2021-08-02 19:06:38 -04:00
parent 5fab51b47c
commit 530339f971
1 changed files with 31 additions and 19 deletions

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@ -14,6 +14,7 @@
\usepackage{graphicx} \usepackage{graphicx}
\usepackage{subcaption} \usepackage{subcaption}
\usepackage{nth} \usepackage{nth}
\usepackage{hyperref} % must be before cleveref
\usepackage[capitalize]{cleveref} \usepackage[capitalize]{cleveref}
\usepackage[version=4]{mhchem} \usepackage[version=4]{mhchem}
\usepackage{pgfgantt} \usepackage{pgfgantt}
@ -160,6 +161,7 @@
\newacronym{zfn}{ZFN}{zinc-finger nuclease} \newacronym{zfn}{ZFN}{zinc-finger nuclease}
\newacronym{talen}{TALEN}{transcription activator-like effector nuclease} \newacronym{talen}{TALEN}{transcription activator-like effector nuclease}
\newacronym{qbd}{QbD}{quality-by-design} \newacronym{qbd}{QbD}{quality-by-design}
\newacronym{aws}{AWS}{amazon web services}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SI units for uber nerds % 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} \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 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 \gls{dms} system, we developed a program to curate and aggregate the raw
datafiles into a \gls{sql} database (\cref{fig:meta_overview}). 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 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 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 in a Postgres database (specifically Aurora implementation hosted on \gls{aws}).
source data (for example, flagging entries which had a reagent whose This program included checks to ensure the integrity of source data (for
manufacturing date was after the date the experiment started, which signifies a example, flagging entries which had a reagent whose manufacturing date was after
human input error). the date the experiment started, which signifies a human input error).
\subsection{statistical analysis}\label{sec:statistics} \subsection{statistical analysis}\label{sec:statistics}
@ -4341,10 +4331,32 @@ expansion technology given that even in healthy donors, we observed the
\onecolumn \onecolumn
\clearpage \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} The code used to aggregate all experimental data was written primarily in
\renewcommand{\section}[2]{} % noop the original bib section header 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} \bibliography{references}