ADD method for meta-analysis

tex/thesis.tex

@@ -100,6 +100,8 @@
 \newacronym{moi}{MOI}{multiplicity of infection}
 \newacronym{ifng}{IFN$\upgamma$}{interferon-$\upgamma$}
 \newacronym{tnfa}{TNF$\upalpha$}{tumor necrosis factor-$\upalpha$}
+\newacronym{sql}{SQL}{structured query language}
+\newacronym{fcs}{FCS}{flow cytometry standard}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % SI units for uber nerds
@@ -1056,6 +1058,34 @@ via a Biorad Bioplex 200 plate reader.
   \input{../tables/luminex_panel.tex}
 \end{table}
 
+\subsection{data aggregation and meta-analysis}
+
+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.
+
+% FIGURE summarize this stuff in a picture
+
+The data files to be aggregated included Microsoft Excel files which held
+timeseries measurements for cell cultures (eg cell counts, viability, glucose,
+\gls{il2} added, media added, and media removed), \gls{fcs} files for cellular
+phenotypes, and FlowJo files which held gating parameters and statistics based
+on the \gls{fcs} files. Additional information which was held in electronic lab
+notebooks (eg OneNote files) was not easily parsable, and thus this data was
+summarized in YAML files. The data included in these YAML files included reagent
+characteristics (vendor, catalog number, lot number, manufacturing date), cell
+donor characteristics (age, \gls{bmi}, phenotype, demographic, gender), and all
+experimental parameters such as the number of bead or \gls{dms} added.
+
+% FIGURE data model
+
+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).
+
 \subsection{statistical analysis}
 
 For 1-way \gls{anova} analysis with Tukey multiple comparisons test,
@@ -1077,9 +1107,6 @@ lack-of-fit tests where replicates were present (to assess model fit in the
 context of pure error). Statistical significance was evaluated at $\upalpha$ =
 0.05.
 
-% METHOD add meta-analysis
-% METHOD add Grex
-
 \section{results}
 
 \subsection{DMSs can be fabricated in a controlled manner}