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    1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    2 %                                                                             %
    3 % Copyright (C) 2013-2014 Edward d'Auvergne                                   %
    4 %                                                                             %
    5 % This file is part of the program relax (http://www.nmr-relax.com).          %
    6 %                                                                             %
    7 % This program is free software: you can redistribute it and/or modify        %
    8 % it under the terms of the GNU General Public License as published by        %
    9 % the Free Software Foundation, either version 3 of the License, or           %
   10 % (at your option) any later version.                                         %
   11 %                                                                             %
   12 % This program is distributed in the hope that it will be useful,             %
   13 % but WITHOUT ANY WARRANTY; without even the implied warranty of              %
   14 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               %
   15 % GNU General Public License for more details.                                %
   16 %                                                                             %
   17 % You should have received a copy of the GNU General Public License           %
   18 % along with this program.  If not, see <http://www.gnu.org/licenses/>.       %
   19 %                                                                             %
   20 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   21 
   22 
   23 \begin{center}
   24 \begin{small}
   25 
   26 % The longtable environment.
   27 \latex{\LTcapwidth=\textwidth}
   28 \begin{longtable}{l@{\extracolsep{\fill}}ccccccccc}
   29 
   30 % Caption.
   31 \caption[Dispersion software comparison.]{Comparison of the features for the different dispersion software.}
   32 
   33 
   34 % Header.
   35 \\
   36 \toprule
   37 \vspace{25pt} \\
   38    & \begin{rotate}{45}CPMGFit\end{rotate} & \begin{rotate}{45}cpmg\_fit\end{rotate} & \begin{rotate}{45}CATIA\end{rotate} & \begin{rotate}{45}NESSY\end{rotate} & \begin{rotate}{45}GUARDD\end{rotate} & \begin{rotate}{45}ShereKhan\end{rotate} & \begin{rotate}{45}GLOVE\end{rotate} & \begin{rotate}{45}chemex\end{rotate} & \begin{rotate}{45}relax\end{rotate} \hspace{5pt} \\
   39 %        & CPMGFit & CATIA & NESSY & GUARDD & ShereKhan & GLOVE & relax \\
   40 \midrule
   41 \endhead
   42 
   43 % Footer.
   44 \bottomrule
   45 \endfoot
   46 
   47 % Label.
   48 \label{table: dispersion software}
   49 
   50 %est row                    & \yes & \yes & \yes & \yes & \yes & \yes & \yes & \yes & \yes \\
   51 
   52 % The models.
   53 \vspace{-5pt} \\
   54 \textbf{Dispersion models} \\
   55 \latex{\cmidrule(lr){1-1}}
   56 \vspace{-5pt} \\
   57 Base models \\
   58 \latex{\cmidrule(lr){1-1}}
   59 $\Rtwoeff/\Ronerhoprime$    & \no  & \no  & \no  & \yes & \yes & \yes & \yes & \no  & \yes \\
   60 No Rex                      & \no  & \yes & \no  & \yes & \yes & \no  & \yes & \no  & \yes \\
   61 
   62 \vspace{-5pt} \\
   63 Single quantum (SQ) CPMG-type \\
   64 \latex{\cmidrule(lr){1-1}}
   65 LM63                        & \yes & \no  & \no  & \yes & \no  & \yes & \yes & \no  & \yes \\
   66 LM63 3-site                 & \yes & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \yes \\
   67 CR72                        & \yes & \no  & \no  & \yes & \no  & \yes & \yes & \no  & \yes \\
   68 IT99                        & \yes & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \yes \\
   69 TSMFK01                     & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   70 B14                         & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   71 NS 2-site                   & \no  & \yes & \yes & \no  & \no  & \yes & ?    & \no  & \yes \\
   72 
   73 \vspace{-5pt} \\
   74 MMQ (SQ, ZQ, DQ, \& MQ) CPMG-type \\
   75 \latex{\cmidrule(lr){1-1}}
   76 MMQ CR72                    & \no  & \yes & \no  & \no  & \yes & \no  & ?    & \no  & \yes \\
   77 NS MMQ 2-site               & \no  & \yes & \no  & \no  & \no  & \no  & ?    & \no  & \yes \\
   78 NS MMQ 3-site linear        & \no  & \yes & \no  & \no  & \no  & \no  & ?    & \no  & \yes \\
   79 NS MMQ 3-site               & \no  & \yes & \no  & \no  & \no  & \no  & ?    & \no  & \yes \\
   80 
   81 \vspace{-5pt} \\
   82 $\Ronerho$-type \\
   83 \latex{\cmidrule(lr){1-1}}
   84 M61                         & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   85 DPL94                       & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   86 TP02                        & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   87 TAP03                       & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   88 TP04                        & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  \\
   89 MP05                        & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   90 BK13                        & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  \\
   91 NS $\Ronerho$ 2-site        & \no  & \yes & \no  & \no  & \no  & \no  & ?    & \no  & \yes \\
   92 NS $\Ronerho$ 3-site linear & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   93 NS $\Ronerho$ 3-site        & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
   94 
   95 \midrule
   96 \vspace{-5pt} \\
   97 \textbf{General features} \\
   98 \latex{\cmidrule(lr){1-1}}
   99 Parallelisation via MPI for running on clusters & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
  100 Off-resonance effects (CPMG-type data)          & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  \\
  101 Off-resonance effects ($\Ronerho$-type data)    & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
  102 Support for TROSY-type data                     & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  \\
  103 Support for CEST-type data                      & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes & \no  \\
  104 Support for scalar coupling effects             & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  \\
  105 Arrhenius / Van't Hoff analysis                 & \no  & \yes & \no  & \yes & \yes & \no  & \no  & \no  & \no  \\
  106 Dispersion data back calculation (BC)           & \no  & \yes & \no  & \yes & \yes & \no  & \no  & \no  & \yes \\
  107 
  108 \pagebreak
  109 
  110 \vspace{-5pt} \\
  111 \textbf{User interface} \\
  112 \latex{\cmidrule(lr){1-1}}
  113 Graphical user interface (GUI)                  & \no  & \no  & \no  & \yes & \yes & \no  & \no  & \no  & \yes \\
  114 Web user interface (Web UI)                     & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  \\
  115 Scripting user interface (Script UI)            & \no  & \yes & \yes & \no  & \no  & \yes & \yes & \no  & \yes \\
  116 Shell interface                                 & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \yes & \no  \\
  117 Temperature and field-dependent simulator     \\
  118 UI for experimental planning (data BC)          & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \no  \\
  119 
  120 \vspace{-5pt} \\
  121 \textbf{Optimisation} \\
  122 \latex{\cmidrule(lr){1-1}}
  123 Grid search algorithm                           & \yes & \no  & \no  & \yes & \yes & \yes & \yes & \no  & \yes \\
  124 Grid search (via scripting)                     & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \no  & \no  \\
  125 Nelder-Mead simplex algorithm                   & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
  126 Levenberg-Maquardt algorithm                    & \yes & \yes & \yes & \yes & \no  & \yes & \yes & \yes & \no  \\
  127 Numeric gradient approximation                  & \yes & \yes & \yes & \yes & \no  & \yes & \yes & \yes & \no  \\
  128 Logarithmic-barrier constraint algorithm        & \no  & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \yes \\
  129 MATLAB interior-point black magic               & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \no  \\
  130 Visualisation of the chi-squared space          & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \yes \\
  131 
  132 \vspace{-5pt} \\
  133 \textbf{Error propagation} \\
  134 \latex{\cmidrule(lr){1-1}}
  135 Covariance matrix (lowest quality)              & \yes & \yes & \yes & \no  & \yes & \yes & \yes & \no  & \no  \\
  136 Jackknife simulations (for missing errors)      & \yes & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \no  \\
  137 Bootstrapping simulations (false errors)        & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  \\
  138 Monte Carlo simulations (gold standard)         & \yes & \no  & \no  & \yes & \yes & \no  & \yes & \yes & \yes \\
  139 
  140 \vspace{-5pt} \\
  141 \textbf{Inbuilt statistical comparisons} \\
  142 \latex{\cmidrule(lr){1-1}}
  143 Akaike's Information Criterion (AIC)            & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \yes \\
  144 Small sample size AIC (AICc)                    & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \no  & \yes \\
  145 Bayesian Information Criterion (BIC)            & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \yes \\
  146 F-testing (ANOVA statistics)                    & \no  & \no  & \no  & \yes & \yes & \no  & \no  & \no  & \no  \\
  147 
  148 \vspace{-5pt} \\
  149 \textbf{Data and model testing} \\
  150 \latex{\cmidrule(lr){1-1}}
  151 Insignificant dispersion curve tests            & \no  & \no  & \no  & \yes  & \no  & \no  & \no  & \no  & \yes \\
  152 Model elimination tests                         & \no  & \no  & \no  & \no   & \no  & \no  & \no  & \no  & \yes \\
  153 
  154 \vspace{-5pt} \\
  155 \textbf{Programming languages} \\
  156 \latex{\cmidrule(lr){1-1}}
  157 Python                      & \no  & \no  & \no  & \yes & \no  & \yes & \no  & \yes & \yes \\
  158 C                           & \no  & \yes & \yes & \no  & \no  & \no  & \yes & \no  & \yes \\
  159 Perl                        & \no  & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \no  \\
  160 MATLAB                      & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  & \no  \\
  161 FORTRAN                     & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  \\
  162 Ruby on Rails               & \no  & \no  & \no  & \no  & \no  & \yes & \no  & \no  & \no  \\
  163 
  164 \vspace{-5pt} \\
  165 \textbf{Free software licencing} \\
  166 \latex{\cmidrule(lr){1-1}}
  167 GNU General Public Licence (version 2+)     & \yes & \no  & \no  & \no  & \no  & \no  & \no  & \no  & \no  \\
  168 GNU General Public Licence (version 3+)     & \no  & \no  & \no  & \yes & \yes & \no  & \no  & \yes & \yes \\
  169 Free software infrastructure                & \no  & \no  & \no  & \yes & \yes & \no  & \no  & \yes & \yes \\
  170 Proprietary                                 & \no  & \yes & \yes & \no  & \no  & \yes & \yes & \no  & \no  \\
  171 
  172 \end{longtable}
  173 \end{small}
  174 \end{center}