% Citations.
%%%%%%%%%%%%

\chapter{Citations} \label{ch: citations}

As relax is a large collection of work created by diverse authors, care must be taken to properly cite the parts which you use.  The following is a breakdown of all of the citations relating to relax, including the basic citations for the various analysis types.



% The software relax.
%%%%%%%%%%%%%%%%%%%%%

\section{The software relax}


% relax.
%~~~~~~~

\subsection{relax references}

The primary citations for relax are:

\begin{itemize}
\item \bibentry{dAuvergneGooley08a}
\item \bibentry{dAuvergneGooley08b}
\end{itemize}


% Graphical user interface.
%~~~~~~~~~~~~~~~~~~~~~~~~~~

\subsection{Graphical user interface reference}

The primary citation for the GUI is:

\begin{itemize}
\item \bibentry{Bieri11}
\end{itemize}


% The multi-processor.
%~~~~~~~~~~~~~~~~~~~~~

\subsection{The multi-processor reference}

Although not published, if the multi-processor framework is used to run relax on multi-core systems, grids, or clusters, then please acknowledge the author of that code -- Gary Thompson.



% Specific analyses.
%%%%%%%%%%%%%%%%%%%%

\section{Specific analyses}

The following subsections list the citations for the individual analysis specific parts of relax.


% Model-free analysis.
%~~~~~~~~~~~~~~~~~~~~~

\subsection{Model-free analysis references}

The base citations for model-free theory are:

\begin{itemize}
\item \bibentry{LipariSzabo82a}
\item \bibentry{LipariSzabo82b}
\item \bibentry{Clore90a}
\end{itemize}

If the automated analysis of the \file{dauvergne\_protocol.py} sample script or the GUI model-free analysis which uses the same protocol has been used, then the following citations are all implicit:

\begin{itemize}
\item \bibentry{dAuvergneGooley03}
\item \bibentry{dAuvergneGooley06}
\item \bibentry{dAuvergneGooley07}
\item \bibentry{dAuvergneGooley08a}
\item \bibentry{dAuvergneGooley08b}
\end{itemize}

Otherwise, if model-free analysis is used in relax but not via the inbuilt automated protocol, the first reference is for model selection, the second is for eliminating failed model-free models, and the forth is for the optimisation improvements (the third and fifth are for the automated protocol).  All of the model-free implementation details of relax are covered by the PhD thesis (available as a PDF or as a printed version on Amazon.com) of:

\begin{itemize}
\item \bibentry{dAuvergne06}
\end{itemize}

The reference for the hybridisation of different global diffusion models to analyse the residual inter-domain dynamics -- a not very well documented feature of relax -- is:

\begin{itemize}
\item \bibentry{Horne07}
\end{itemize}

If the softwares Modelfree4 or Dasha are used as replacement optimisation engines from within relax, the citations for Modelfree4 are:

\begin{itemize}
\item \bibentry{Palmer91}
\item \bibentry{Mandel95}
\end{itemize}

and for Dasha:

\begin{itemize}
\item \bibentry{Orekhov95a}
\end{itemize}


% Consistency testing analysis.
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

\subsection{Consistency testing analysis references}

The base citations for the consistency testing of NMR relaxation is:

\begin{itemize}
\item \bibentry{Fushman99}
\item \bibentry{Farrow95}
\item \bibentry{Fushman98}
\end{itemize}

The first is the main citation, whereas the next are the individual tests.  The citation for the consistency testing of NMR relaxation as implemented in relax is:

\begin{itemize}
\item \bibentry{MorinGagne09a}
\end{itemize}


% N-state model analysis.
%~~~~~~~~~~~~~~~~~~~~~~~~

\subsection{N-state model analysis references}

Some citations demonstrating as well as presenting the use of the N-state model for diverse analyses types are:

\begin{itemize}
\item \bibentry{Sun11}
\item \bibentry{Erdelyi11}
\end{itemize}


% Reduced spectral density mapping.
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

\subsection{Reduced spectral density mapping references}

The base citations for reduced spectral density mapping are:

\begin{itemize}
\item \bibentry{Farrow95}
\item \bibentry{Lefevre96}
\end{itemize}



% Generic parts of relax.
%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Generic parts of relax}

The following subsections will list the citations for the parts of relax independent of the specific analyses.


% Model selection.
%~~~~~~~~~~~~~~~~~

\subsection{Model selection references}

The citation for the model selection component of relax is:

\begin{itemize}
\item \bibentry{dAuvergneGooley03}
\end{itemize}

The base citations for the specific model selection techniques of AIC, AICc, and BIC are respectively:

\begin{itemize}
\item \bibentry{Akaike73}
\item \bibentry{HurvichTsai89}
\item \bibentry{Schwarz78}
\end{itemize}



% Other citations.
%%%%%%%%%%%%%%%%%%

\section{Other citations}

If you believe that other citations should be included in this chapter, please contact the relax users mailing list (relax-users at gna.org\index{mailing list!relax-users}).

