supplementary_materials.tex

\RequirePackage{fix-cm}
%
%\documentclass{svjour3}                     % onecolumn (standard format)
%\documentclass[smallcondensed]{svjour3}     % onecolumn (ditto)
\documentclass[smallextended]{svjour3}       % onecolumn (second format)
%\documentclass[twocolumn]{svjour3}          % twocolumn
%
\smartqed  % flush right qed marks, e.g. at end of proof
%
\usepackage{graphicx}
%
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{upquote,textcomp}
\usepackage{hyperref}
\newcommand{\code}[1]{\texttt{#1}}

\journalname{Behavior Research Methods}

\begin{document}

\title{PyMICE -- a Python library for analysis of IntelliCage data
}
\subtitle{Supplementary materials}

\titlerunning{Supplementary materials for PyMICE -- a Python library...}

\author{Jakub M. Dzik \and
        Alicja Puścian \and
        Zofia Mijakowska \and
        Kasia Radwanska \and
        Szymon Łęski
}

\institute{J. M. Dzik \and A. Puścian \and S. Łęski \at
              Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland \\
           \and
           Z. Mijakowska \and K. Radwanska \at
              Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
           \and
           S. Łęski \at \email{s.leski@nencki.gov.pl}
}

\maketitle

\begin{abstract}
We provide our readers with resources and guidance necessary to reproduce
the presented results.

\keywords{Reproducible research \and Literate programming \and Python scripts \and raw data}
\end{abstract}

\tableofcontents
\newpage

\section{Introduction}
In order to meet the standarts of reproducibility and enable a \emph{reproducibility
review}~\cite{peng2011} we decided to publish the data, scripts, and complete
source of the article~\cite{buckheit1995,literateProgramming}.


\section{Requirements}
\input{supplementary_reproducibility}


\section{Reproduction of the examples}
\label{examples}

\subsection{Obtaining the example data}
\label{examples:data}
In order to save the example data in the working directory, run the
\emph{get\_example\_data.py} script:
\begin{verbatim}
$ python get_example_data.py
\end{verbatim}

However, the files are also available as supplementary materials (see
\ref{data:examples} for details).

\subsection{Example 1}
\label{examples:1}
In order to reproduce the 6-line example of data analysis, provide the
\emph{demo.zip} file (\ref{data:examples:demo}) in the working directory and
run the \emph{example1.py} script:
\begin{verbatim}
$ python example1.py
\end{verbatim}


\subsection{Example 2}
\label{examples:2}
To reproduce plot from \emph{Example 2},
provide the \emph{FVB} dataset (\ref{data:examples:fvb}) in the working
directory and run the \emph{example2.py} script:
\begin{verbatim}
$ python example2.py
\end{verbatim}


\subsection{Example 3}
\label{examples:3}
To reproduce plot from \emph{Example 3} (also figure 3A in~\cite{Puscian:2014cu}),
provide the \emph{C57\_AB} dataset (\ref{data:examples:c57}) in the working
directory and run the \emph{example3.py} script:
\begin{verbatim}
$ python example3.py
\end{verbatim}


\subsection{Example 4}
\label{examples:4}
To reproduce plot from \emph{Example 4} provide the \emph{C57\_AB}
dataset (\ref{data:examples:c57}) in the working directory and run the
\emph{example4.py} script:
\begin{verbatim}
$ python example4.py
\end{verbatim}


\section{Reproduction of the article}
\label{reproduction}
To automatically generate a custom version of the article based on reproduced
results rather than on the results claimed by the authors, perform the following
procedure: extract the contents of the
\emph{article\_source.zip} archive to the working directory.

In case the \emph{GNU Make} tool (or similar) is installed in the system, to
reproduce the article run:
\begin{verbatim}
$ make article.pdf
\end{verbatim}

If \emph{GNU Make} tool is not installed, you need to weave~\cite{literateProgramming}
the \emph{texw} files.
It is important to weave \emph{get\_example\_data.texw} as the first file,
since example data (\ref{data:examples}) are saved in the working directory
during its weaving.

\begin{verbatim}
$ Pweave -f tex get_example_data.texw
$ Pweave -f tex pymice_overview.texw
$ Pweave -f tex pymice_reproducibility.texw
$ Pweave -f tex example1.texw
$ Pweave -f tex -F figures example2.texw
$ Pweave -f tex -F figures example3.texw
$ Pweave -f tex -F figures example4.texw
\end{verbatim}

After all files have been weaved, compile the \LaTeX{} source.

\begin{verbatim}
$ pdflatex article.tex
$ bibtex article
$ pdflatex article.tex
$ pdflatex article.tex
\end{verbatim}

The \emph{article.pdf} file contains the reproduced article.


\section{Description of datasets}
\subsection{Datasets used in the examples}
\label{data:examples}


\subsubsection{demo.zip}
\label{data:examples:demo}
\emph{demo.zip} is a dataset prepared for demonstration purposes.
It is required by \emph{example1.py} script (\ref{examples:1}).


\subsubsection{FVB}
\label{data:examples:fvb}
The dataset concerning reward discrimination learning of FVB mice was obtained
during an ongoing research project and thus has not yet been published. For
that reason data were preprocessed to both anonimise it and make it more
suitable for demonstrational purposes. However, it should be stated that
presented data had actually been acquired with the use of FVB strain.

The dataset consist of one data file
and experiment timeline:
\begin{itemize}
\item \emph{2016-07-20~10.11.11.zip}
\item \emph{timeline.ini}
\end{itemize}
and is required by \emph{example2.py} (\ref{examples:2}).


\subsubsection{C57\_AB}
\label{data:examples:c57}
The \emph{C57\_AB} dataset was obtained during an actual research
project~\cite{Puscian:2014cu} and processed to make it suitable for more advanced
demonstrational purposes. It consist of four data files and experiment
timeline:
\begin{itemize}
\item \emph{2012-08-28~13.44.51.zip}
\item \emph{2012-08-28~15.33.58.zip}
\item \emph{2012-08-31~11.46.31.zip}
\item \emph{2012-08-31~11.58.22.zip}
\item \emph{timeline.ini}
\end{itemize}
and is required by
\emph{example3.py} (\ref{examples:3}) and
\emph{example4.py} (\ref{examples:4}).


\subsection{Dataset discussed in the \emph{PyMICE library} section}
\emph{2014-09-11~14.13.34.zip} is a raw dataset obtained during an actual
research project by Maria Nalberczak from laboratory of KR.

The discussed 6-hour period starts at 22:00 (\mbox{UTC-08:00})
\mbox{2014-09-11}.
For mouse `9' the Analyzer software (v.~2.11.0.0) reports 480 licks less
than the number counted with PyMICE. The dataset has been inspected
manually. It seems that if the recorded start time of a nosepoke precedes the
recorded start time of the related visit, it will be omited by the Analyzer.

\begin{acknowledgements}
\input{pymice_acknowledgements}
\end{acknowledgements}

%\bibliographystyle{spbasic}      % basic style, author-year citations
\bibliographystyle{spmpsci}      % mathematics and physical sciences
%\bibliographystyle{spphys}       % APS-like style for physics
\bibliography{pymice}            % name your BibTeX data base

\end{document}