init

Author: qgeissmann

.gitignore

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+*.log
+*.dvi
+*.aux
+*.out
+*.bbl
+*.dvi
+*.pdf
+!thesis.pdf
+*.blg
+*.toc
+*.pyg
+*.acn
+*.acr
+*.alg
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.ist
+*.fls
+*.fdb_latexmk
+*.synctex.gz
+*.tdo
+*.lof
+*.lot
+autogenerated-tutorial*
+cache/

.latexmkrc

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+# Usage: latexmk report.tex
+# Inspired by https://github.com/cdlm/infrastructure/blob/master/dotfiles/latexmkrc
+$pdf_mode = 1;
+$pdflatex = 'xelatex --shell-escape -file-line-error -halt-on-error -synctex=1 %O %S';
+
+# http://tex.stackexchange.com/questions/1226/how-to-make-latexmk-use-makeglossaries
+add_cus_dep('glo', 'gls', 0, 'run_makeglossaries');
+add_cus_dep('acn', 'acr', 0, 'run_makeglossaries');
+push @generated_exts, 'glo', 'gls', 'glg';
+push @generated_exts, 'acn', 'acr', 'alg';
+$clean_ext .= ' %R.ist %R.xdy';
+
+sub run_makeglossaries {
+  if ( $silent ) {
+    system "makeglossaries -q '$_[0]'";
+  }
+  else {
+    system "makeglossaries '$_[0]'";
+  };
+}

1-intro/1-intro.tex

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+\begin{figure}[h!]
+	\includegraphics[width=0.95\textwidth]{\currfiledir/.\currfilebase.pdf}
+
+	\caption[Drosophila Activity Monitor]{\ctit{Drosophila Activity Monitor.}
+		\textbf{A}: a Drosophila Activity Monitor (DAM), the most widely used system to monitor walking activity and sleep in \droso, with 8 tubes loaded.
+		Each monitor can hold up to 32 single flies in glass tubes.
+		Multiple monitors can run in parallel, and their data is centralised on an acquisition computer.
+		\textbf{B}: Schematic of a single tube ($\approx 70$~mm long) showing the underlying mechanism of the DAM.
+		Each fly is contained between food on one side and cotton wool on the other. 
+		Tubes are sealed with paraffin wax.
+		When the fly walks through the midline of its tube, it crosses an infrared beam which is detected as movement.
+		The numbers of beam crosses are generally aggregated over one minute (\ie{} the resulting sampling rate being 1~min$^{-1}$).
+		\label{fig:\currfilebase}
+	}
+\end{figure}