Author: bugman
Date: Tue Aug 28 17:29:48 2012
New Revision: 17362
URL: http://svn.gna.org/viewcvs/relax?rev=17362&view=rev
Log:
Created the new 'Citations' chapter of the relax user manual.
This is to clearly outline to the user the citations required for the various
components of relax.
Added:
trunk/docs/latex/cite.tex
Modified:
trunk/docs/latex/relax.tex
Added: trunk/docs/latex/cite.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/cite.tex?rev=17362&view=auto
==============================================================================
--- trunk/docs/latex/cite.tex (added)
+++ trunk/docs/latex/cite.tex Tue Aug 28 17:29:48 2012
@@ -1,0 +1,188 @@
+% Citations.
+%%%%%%%%%%%%
+
+\chapter{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}
+
+The primary citations for relax are:
+
+\begin{itemize}
+\item \bibentry{dAuvergneGooley08a}
+\item \bibentry{dAuvergneGooley08b}
+\end{itemize}
+
+
+
+% Graphical user interface.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Graphical user interface}
+
+The primary citation for the GUI is:
+
+\begin{itemize}
+\item \bibentry{Bieri11}
+\end{itemize}
+
+
+
+% The multi-processor.
+%~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{The multi-processor}
+
+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}
+
+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 \texttt{`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}
+
+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}
+
+The base citation for the consistency testing of NMR relaxation is:
+
+\begin{itemize}
+\item \bibentry{Fushman99}
+\end{itemize}
+
+The citation for the consistency testing of NMR relaxation as implemented in
relax is:
+
+\begin{itemize}
+\item \bibentry{MorinGagne09}
+\end{itemize}
+
+
+
+% N-state model analysis.
+%~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{N-state model analysis}
+
+Some citations demonstrating and present the use of the N-state model
analysis are:
+
+\begin{itemize}
+\item \bibentry{Sun11}
+\item \bibentry{Erdelyi11}
+\end{itemize}
+
+
+% Reduced spectral density mapping.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Reduced spectral density mapping}
+
+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}
+
+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}).
+
Modified: trunk/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=17362&r1=17361&r2=17362&view=diff
==============================================================================
--- trunk/docs/latex/relax.tex (original)
+++ trunk/docs/latex/relax.tex Tue Aug 28 17:29:48 2012
@@ -71,6 +71,10 @@
% Natbib Citation format.
\bibpunct{(}{)}{;}{a}{,}{,}
+
+% Inline citations.
+\usepackage{bibentry}
+\nobibliography*
% Allow the maths blocks to be broken!!!
\allowdisplaybreaks[1]
@@ -201,6 +205,7 @@
%%%%%%%%%%%%%%%
\include{intro}
+\include{cite}
\include{install}
\include{infrastruct}
\include{data_model}
r17362 - in /trunk/docs/latex: cite.tex relax.tex