%--*- latex -*-----------------------------------------------------------------
%$Author: saulius $
%$Date: 2013-07-18 16:54:42 +0300 (Thu, 18 Jul 2013) $ 
%$Revision: 587 $
%$URL: svn+ssh://saulius-grazulis.lt/home/saulius/svn-repositories/seminarai/2013-Mol%C4%97tai/slides.mltex $
%------------------------------------------------------------------------------

\documentclass[mathserif]{beamer}
\usepackage{rotating}
%% \usefonttheme{structurebold}
%% \usetheme{Antibes}
%% \usetheme{Bergen}
\usetheme{Marburg}
\useoutertheme{infolines}
\setbeamertemplate{headline}{} % removes the headline that infolines inserts
\setbeamertemplate{footline}[frame number]

\definecolor{SOLSAbg}{HTML}{4E5B6F}
\setbeamercolor{sidebar canvas right}{bg=SOLSAbg}
\setbeamertemplate{sidebar canvas right}[horizontal shading]
    [top=SOLSAbg,bottom=SOLSAbg]

\setbeamersize{sidebar width right=1cm}
\setbeamertemplate{sidebar right}{
  \hspace{\baselineskip}
  \begin{sideways}
    \parbox{8cm}{
      \tiny\sf
      \raggedright
      This project has received funding from the European Union's
      Horizon 2020 \\
      research and innovation program under grant agreement
      No 689868.
    }
  \end{sideways}
}

%% \usepackage{txfonts}
%% \renewcommand\rmdefault{pbk}
%% \renewcommand\rmdefault{ptm}
%% \renewcommand\rmdefault{ppl}
%% \renewcommand\rmdefault{pnc}
%% \setbeamerfont{title}{family=\rmfamily}
%% \usepackage{lucidaso}       % Lucida Bright (SO Version)
%% \usepackage{lucidabr}       % Lucida Bright
%% \usepackage[small]{eulervm} % Euler VM
\usepackage[utf8x]{inputenc}
\usepackage{bookman}
\renewcommand\familydefault{\rmdefault}
\usepackage[T1]{fontenc}

\usepackage{colordvi}
\usepackage{graphicx}
\usepackage{tikz}
\usetikzlibrary{snakes}
\usetikzlibrary{shapes,arrows}
\usepackage{verbatim}
\usepackage{fancyvrb}
\usepackage{listings}
%% \usepackage{chemfig}

\include{commands}

\newcommand{\RCSid}[1]{\fontsize{7pt}{7pt}\selectfont $#1$ \today}

\logo{
  \includegraphics[height=1.5cm]{images/SOLSA-EU.eps.gz}
}

\title{The Crystallography Open Database – new perspectives}

\author{\scriptsize\underline{Saulius Gražulis}
\and  Andrius Merkys
\and  Antanas Vaitkus
}

\date{Leiden, CECAM 2016}

\begin{document}

%------------------------------------------------------------------------------

\begin{frame}
    \insertlogo\titlepage

    \centerline{\scriptsize Vilnius University Institute of Biotechnology}

    \begin{center}
      \mbox{}
      \hfill\hfill\hfill
      \includegraphics[height=1.5cm]{images/sp_VU_zenklas.eps}
      \hfill
      \includegraphics[height=1.5cm]{images/BTI-logo-no-text.eps}
      \hfill\hfill\hfill
      \mbox{}
    \end{center}

    \vfill

%%     \RCSid{
%%       $Id: slides.mltex 587 2013-07-18 13:54:42Z saulius $
%%     }
\end{frame}

%==============================================================================

\begin{frame}
  \frametitle{Open Crystallographic Databases}
  \framesubtitle{COD, TCOD, PCOD, MPOD, ...}

  \begin{centering}

    \hfill
    \begin{minipage}{5cm}
      \begin{center}
        \includegraphics[width=\textwidth]{images/cod.eps.gz} \\
        {\scriptsize\mywebref{http://www.crystallography.net/cod}} \\
        \footnotesize
        $> 367\,000$ entries (ready to grow $> 10^6$?)
      \end{center}
    \end{minipage}
    \hfill
    \begin{minipage}{5cm}
      \begin{center}
        \includegraphics[width=\textwidth]{images/tcod.eps.gz} \\
        {\scriptsize\mywebref{http://www.crystallography.net/tcod}} \\
        \footnotesize
        $> 2000$ entries (ready to grow to $> 350\,000$?)
      \end{center}
    \end{minipage}
    \hfill

    \begin{minipage}{4cm}
      \begin{center}
        \includegraphics[width=4cm]{images/mpod.eps.gz} \\
        {\scriptsize\mywebref{http://mpod.cimav.edu.mx/}} \\
        \footnotesize
        $> 300$ entries
      \end{center}
    \end{minipage}
    %%
    \begin{minipage}{6cm}
      \begin{center}
        \begin{tikzpicture}
          \node (PCOD) at (0,0) {\includegraphics[width=4cm]{images/pcod.eps.gz}};
          \node (PCOD) at (2.2,-1) {\includegraphics[width=2cm]{images/pcodsmall.eps.gz}};
        \end{tikzpicture} \\
        {\scriptsize\mywebref{http://www.crystallography.net/pcod}} \\
        \footnotesize
        $> 10^6$ entries (ready to grow to $> 10^8$?)
      \end{center}
    \end{minipage}

  \end{centering}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{COD 13 years later}

  \vskip 0.5\baselineskip
  COD increased 7-fold; currently contains over 367000 records (Sept. 2016)

  \vspace{-0.5\baselineskip}
  \begin{center}
    \includegraphics[width=6cm,angle=-90]{data/outputs/cod-record-numbers-graph.eps}
  \end{center}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{Commong framework: the CIF}

  \scriptsize
  The Crystallographic Interchange Framework (CIF) is developed and curated
  by the International Union of Crystallography (IUCr).

  \showfile[basicstyle=\ttfamily\tiny]{examples/data/2100858-head.cif}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}[containsverbatim]
  \frametitle{Description of semantics}
  \framesubtitle{CIF dictionaries}

  \tiny
  \verbatiminput{examples/cif_core_cell_length.dic}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}[containsverbatim]
  \frametitle{TCOD dictionary contents}
  \framesubtitle{The most basic data names}

  \footnotesize
  \begin{itemize}
    \item \texttt{cif\_tcod.dic}: ver.\ 0.008, last update 2015-06-16,
      107 data names;

    \item \texttt{cif\_dft.dic}: ver.\ 0.019, last update 2016-04-13,
      87 data names.
  \end{itemize}

  e.g. (same as NOMAD
  \myhref{https://nomad-dev.rz-berlin.mpg.de/ui/index.html\#/common/atom\_forces}{atom\_forces}?):

\scriptsize
\begin{verbatim}
data_tcod_atom_site_residual_force
loop_ _name
'_tcod_atom_site_resid_force_Cartn_x'
'_tcod_atom_site_resid_force_Cartn_y'
'_tcod_atom_site_resid_force_Cartn_z'
# ... some names omitted for brevity
_type numb
_units eV/\%A
_units_detail 'electronvolts per Angstroem'
_definition
;
These data items describe residual forces on atoms in the final
structure. For a converged computation of a stable structure these
...
;
\end{verbatim}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}[containsverbatim]
  \frametitle{New developments: CIF2}

  \begin{itemize}
    \item Support of Unicode
      (UTF-8)~\myhref{http://dx.doi.org/10.1107/S1600576715021871}{\cite{Bernstein2016}};
    \item Array data (including multidimensional arrays);
    \item Data hashes (key--value pairs);
    \item Computer readable semantics definitions (in a multiparadigm
      language \texttt{dREL}):
  \end{itemize}

\begin{verbatim}
    _units.code                  angstroms_cubed
    _method.expression
;
    With v as cell_vector
        _cell.volume = v.a * ( v.b ^ v.c )
;
\end{verbatim}

\scriptsize
\mywebref{http://oldwww.iucr.org/iucr-top/cif/ddlm/dREL\_spec\_20071013.html}

\end{frame}

%------------------------------------------------------------------------------

%% \begin{frame}
%%   \frametitle{The COD project}
%% 
%%   %% \tiny
%%   \fontsize{7pt}{9pt}\selectfont
%% 
%%   \fvset{fontseries=b}
%%   \VerbatimInput{text-parts/Michael-Berndt-manifesto.txt}
%% 
%%   \myhref{http://www.cristal.org/SDPD-list/2003/msg00025.html}
%%          {gemstonede (Dr. Michael BERNDT) Fri Feb 14, 2003 1:26 pm}
%% 
%% \end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{COD accessibility}

  COD is a \textbf{fully open-access database}. All records are
  available under public domain designation.

  \vskip\baselineskip
  Provided access methods are:

  \vskip\baselineskip
  \begin{itemize}
    \item Web search
    \item URLs constructed from stable identifiers
    \item RESTful interfaces
    \item Full data download
  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}[containsverbatim]
  \frametitle{COD query examples}
  \framesubtitle{Web, REST, SQL}

  \scriptsize
  \begin{itemize}
    \item Via the WWW interface -- go for ``search'' in:
      \begin{itemize}
        \item \mywebref{http://www.crystallography.net/cod}
        \item \mywebref{http://www.crystallography.net/tcod}
        \item \mywebref{http://www.crystallography.net/pcod}
      \end{itemize}

    \item Via the \textbf{stable} URLs (REST):
      \begin{itemize}
        \item \mywebref{http://www.crystallography.net/cod/2000000.cif}
        \item \mywebref{http://www.crystallography.net/tcod/10000002.cif}
        \item {\fontsize{8.5pt}{8.5pt}\selectfont
          \mywebref{http://www.crystallography.net/cod/result?text=perovskite}}
      \end{itemize}

    \item Via the \textbf{views} of the SQL database:
      \begin{itemize}
        \item 
\footnotesize
\begin{Verbatim}[fontseries=b]
mysql -u cod_reader cod -h www.crystallography.net\
    -e 'select file, a, b, c, vol, formula
        from data where
            date between "2013-01-01" and 
                         "2014-12-31" and
            formula regexp " C[0-9]* "
            order by vol desc limit 10'
\end{Verbatim}
      \end{itemize}
  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{COD applications}

  %% ... Draw a nice illustration of how COD can be used ...
  %% ... Or add URLs of the respective users.

  \small
  \begin{itemize}
    \item SOLSA
      \begin{itemize} \item \mywebref{http://www.solsa-mining.eu/} \end{itemize}
    \item AiiDA \myhref{http://dx.doi.org/10.1016/j.commatsci.2015.09.013}{\cite{Pizzi2016}}
      \begin{itemize} \item \mywebref{http://www.aiida.net/} \end{itemize}
    \item COSMOS \myhref{http://dx.doi.org/10.1021/ci4005282}{\cite{Sadowski2013}}
      \begin{itemize}
        %% \item \mywebref{http://dx.doi.org/10.1021/ci4005282}
        \item \mywebref{http://cdb.ics.uci.edu/}
      \end{itemize}
    \item FPSM
      \myhref{http://dx.doi.org/10.1107/S2053273314009930}{\cite{Boullay2014}},
      MAUD \myhref{http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Boullay_abstract_EMC2012.pdf}{\cite{Boullay2012}}
      \begin{itemize}
        \item \mywebref{http://fpsm.radiographema.com/}
        \item \mywebref{http://maud.radiographema.eu/}
      \end{itemize}
    \item DataWarrior
      \begin{itemize}
        \item \mywebref{http://www.openmolecules.org/datawarrior/}
      \end{itemize}
    \item MolView
      \begin{itemize}
        \item \mywebref{http://molview.org/}
      \end{itemize}
    \item search-match (\myhref{https://www.bruker.com/}{Bruker},
      \myhref{http://www.panalytical.com/}{PANalytical},
      \myhref{http://www.rigaku.com/}{Rigaku})
    \item ... and \myhref{http://wiki.crystallography.net/useful\_links/}{more!}
  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{SOLSA project and COD}

  %% ... Describe the use of COD in the SOLSA project ...

  \definecolor{SolsaGreenArrow}{HTML}{00cc99}

  \vfill
  \parbox[c]{6.5cm}{
    \includegraphics[width=6.5cm]{images/SOLSA-ID-data-flow-scheme.eps.gz}
  }
  {\color{SolsaGreenArrow}$\Leftrightarrow$}
  \parbox[c]{3cm}{
    \includegraphics[width=3.3cm]{images/cod.eps.gz}
  }

  \vspace{2\baselineskip}
  COD will be used in SOLSA for:
  \begin{itemize}
    \item mineral identification;
    \item subsequent data dissemination.
  \end{itemize}

  \vfill
  \vfill
  \scriptsize
  SOLSA data flow diagram courtesy Monique Le Guen, ERAMET.

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{Use of *COD databases}
  \framesubtitle{Search-match identification of the materials}

  \includegraphics[height=6.5cm]{images/search-match.eps.gz}
  \hspace{0.5em}
  \begin{minipage}[b]{2.2cm}
    \raggedright

    \scriptsize A \textbf{predicted} phase from PCOD could be
    identified in experimental data.

    \rule{0pt}{3.9cm}

    \scriptsize
    Courtesy Armel Le Bail \cite{LeBail2008a}
  \end{minipage}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{COD, TCOD and AiiDA link}

  \begin{figure}
    \begin{tikzpicture}[>=stealth]

      \node (AiiDA) at (0,0)
            {\includegraphics[scale=1.25]{images/infrastructure.eps.gz}};

            \node (COD) at (-4,-2.5)
                  {\includegraphics[scale=0.16,angle=0]{images/cod.eps.gz}};
                  \draw[<-,line width=0.5pt] (-2.5,-1) -- (COD.north);

            \node (TCOD) at (3,-2.5)
                  {\includegraphics[scale=0.125,angle=0]{images/tcod.eps.gz}};
                  \draw[->,line width=0.5pt] (0.5,-1) -- (2.15,-2.25);
    \end{tikzpicture}
  \end{figure}

  \scriptsize Courtesy AiiDA developers
  \myhref{http://dx.doi.org/10.1016/j.commatsci.2015.09.013}{\cite{Pizzi2016}}

\end{frame}

%------------------------------------------------------------------------------

%% \begin{frame}
%%   \frametitle{COD Diffraction Image Store}
%% 
%%   \vspace{0.5\baselineskip}
%%   Uses Tahoe-LAFS (\mywebref{https://tahoe-lafs.org}) as a back-end:
%% 
%%   \vspace{-0.5\baselineskip}
%%   \begin{center}
%%     \includegraphics[width=11cm]{images/Tahoe-LAFS-grid.eps.gz}
%%   \end{center}
%% 
%%   Provides:
%% 
%%   \begin{itemize}
%%     \item community-backed store ($\ge$1 PB)
%%     \item confidentiality through strong encryption
%%     \item extreme hardware loss tolerance
%%   \end{itemize}
%% 
%% \end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{*COD data citation}

  % Give an example how COD data can be cited...

  The \myhref{https://www.rd-alliance.org/}{Research Data Alliance}
  has just published and endorsed \textbf{recommendations} from the
  RDA Working Group on Data Citation:
  {\small\mywebref{https://www.rd-alliance.org/groups/data-citation-wg.html}}

  \vspace{0.5\baselineskip}
  COD data can be cited in several ways:

  \begin{itemize}
    \item Using a data reference URI:

      \fbox{
        \begin{minipage}{0.9\textwidth}
          \scriptsize\raggedright
          Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ``Neutron
          Structures of Ammonium Fluoroberyllate'' (1999)
          \textit{The Crystallography Open Database}, rev. 176759, the
          COD Advisory Board (eds.),
          \mywebref{http://www.crystallography.net/cod/2002926.cif}. [Retrieved
            2016-09-21 16:48 EEST]
        \end{minipage}
      }

      \vspace{\baselineskip}

    \item Using a ``landing page'' URI:

      \fbox{
        \begin{minipage}{0.9\textwidth}
          \scriptsize\raggedright
          Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ``Neutron
          Structures of Ammonium Fluoroberyllate'' (1999)
          \textit{The Crystallography Open Database}, rev. 176759,  the
          COD Advisory Board (eds.),
          \mywebref{http://www.crystallography.net/cod/2002926.html}. [Retrieved
            2016-09-21 16:48 EEST]
        \end{minipage}
      }
  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{*COD data citation (2)}

  % Give an example how COD data can be cited...

  COD data can be cited in several ways:

  \begin{itemize}
    \item Using a data reference URI \textbf{with explicit revision}:

      \fbox{
        \begin{minipage}{0.9\textwidth}
          \scriptsize\raggedright
          Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ``Neutron
          Structures of Ammonium Fluoroberyllate'' (1999)
          \textit{The Crystallography Open Database}, rev. 176759, the
          COD Advisory Board (eds.),
          \mywebref{http://www.crystallography.net/cod/2002926.cif@176759}. [Retrieved
            2016-09-21 16:48 EEST]
        \end{minipage}
      }

      \vspace{\baselineskip}

    \item Using a content-negotiable URI (with or without explicit
      revision):

      \fbox{
        \begin{minipage}{0.9\textwidth}
          \scriptsize\raggedright
          Srivastava, R. C.; Klooster, W. T.; Koetzle, T. F. ``Neutron
          Structures of Ammonium Fluoroberyllate'' (1999)
          \textit{The Crystallography Open Database}, rev. 176759, the
          COD Advisory Board (eds.),
          http://www.crystallography.net/cod/2002926. [Retrieved
            2016-09-21 16:48 EEST]
        \end{minipage}
      }

  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}[containsverbatim]
  \frametitle{*COD metadata}

  COD metadata are available in RDF format:

  \mywebref{http://www.crystallography.net/cod/2002926.rdf}

  \lstset{language=xml,morekeywords={cod,rdf}}
  \scriptsize
  \showfile[language=xml,basicstyle=\ttfamily\tiny]{examples/data/2002926-example.rdf}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{Database \textbf{request} citation}

  % Describe how database requests could be cited.

  \vspace{-2\baselineskip}

  \begin{itemize}

    \item
      Data requests (searches) should get their persistent identifiers to
      hide the underlying mechanism:

      \vskip\baselineskip

    {\fontsize{8.5pt}{8.5pt}\selectfont
    http://www.crystallography.net/cod/query/123456  
    }

    $\rightarrow$

    {\fontsize{8.5pt}{8.5pt}\selectfont
      \mywebref{http://www.crystallography.net/cod/result?text=perovskite}}
      

    \item
      Data requests (searches) should be re-runnable on new and old versions
      of the database:

      \vskip\baselineskip

    {\fontsize{8.5pt}{8.5pt}\selectfont
    http://www.crystallography.net/cod/query/567890
    }

    $\rightarrow$

    {\fontsize{7.5pt}{7.5pt}\selectfont
      \mywebref{http://www.crystallography.net/cod/result?text=perovskite\&dbrev=112233}}
      

  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{Software citations?}

  \myhref{https://www.force11.org/}{FORCE11} recommendations:
  \vskip\baselineskip

  Should software be cited? (Yes!) Recommendations published in
  \myhref{https://doi.org/10.7717/peerj-cs.86}{\cite{Smith2016}}

  \begin{itemize}
    \item
      TCOD dictionaries contain data items for versions and names of
      programs and libraries -- additional data items for unique
      identifiers should be provided;

    \item How deep do we need to cite software? Compiler? OS? CPU? How
      reproducible will these be?
  \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame} %% [containsverbatim]
  \frametitle{Interlinked data in COD}

  \begin{center}
    \begin{tikzpicture}

      \node (0,0) (COD site)
            {\includegraphics[width=9cm]{images/COD-external-links.eps.gz}};

      \draw (3.5,0.5) node (MySQL table)
            {\fontsize{5pt}{7pt}\fontseries{b}\fontfamily{\ttdefault}\selectfont
              \input{text-parts/wikipedia-x-cod-example.tex}};

      \draw (0.7,-3) node[ellipse,red,thick,minimum height=0.6cm,minimum
        width=4.2cm,draw] (el) {};

      \draw [->,thick,red] (MySQL table.south) ..
      controls +(0.0,-1.0) and +(1.0,0) .. (el.east); 

    \end{tikzpicture}
  \end{center}

%%   \begin{itemize}
%%     \item LODC
%%     \item COD cross-reference tables
%%   \end{itemize}

\end{frame}

%------------------------------------------------------------------------------

%% \begin{frame}[containsverbatim]
%%   \frametitle{COD completeness challenge}
%% 
%% % The SQL command used to produce the table "text-parts/journals-by-count.txt":
%% 
%% %% select count(*) as nr, journals.name as journal, publishers.name as
%% %% publisher from data join jaltnames on data.journal = jaltnames.altname
%% %% join journals on journal_id = journals.id join publishers on
%% %% publisher_id = publishers.id group by journals.id order by count(*)
%% %% desc limit 15
%% 
%%   \tiny
%%   \fvset{fontseries=b}
%%   \VerbatimInput{text-parts/journals-by-count.txt}
%% 
%% \end{frame}

%------------------------------------------------------------------------------

%% \begin{frame}
%%   \frametitle{COD durability assurance}
%% 
%%   \vspace{1.5\baselineskip}
%%   \begin{itemize}
%%     \item Best price/performance ratio
%%     \item Capability to build a distributed, equal-peer database
%%   \end{itemize}
%% 
%%   \vspace{-2\baselineskip}
%%   \begin{center}
%%     \includegraphics[width=10cm]{images/COD-future-vision_en.eps}
%%   \end{center}
%% 
%% \end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{Acknowledgements}

\small

\begin{minipage}[t]{0.3\textwidth}
\raggedright
\textbf{VU Institute of Biotechnology}
\vspace{\baselineskip}

Virginijus Siksnys ({\em head of the dept.}) \\
\vspace{\baselineskip}

Andrius Merkys \\
Antanas Vaitkus \\
\end{minipage}
%
\begin{minipage}[t]{0.3\textwidth}
\raggedright
\textbf{QM community}
\vspace{\baselineskip}

Björkman Torbjörn \\
Stefaan Cottenier \\
Nicola Marzari \\
Giovanni Pizzi \\
Lubomir Smrcok \\
Linas Vilčiauskas \\
Chris Wolverton \\
\end{minipage}
%
\begin{minipage}[t]{0.35\textwidth}
\raggedright
\textbf{COD Advisory board}
\vspace{\baselineskip}

Daniel Chateigner \\
Robert T. Downs   \\
Werner Kaminsky   \\
Armel Le Bail     \\
Luca Lutterotti   \\
Peter Moeck       \\
Peter Murray-Rust \\
Miguel Quirós
\end{minipage}

\vspace{\baselineskip}
\textbf{Thanks to the Lorentz Center for supporting participation of
  the Vilnius group}

\vspace{\baselineskip}
Thanks to commercial COD users and supporters -- Bruker, PANalytical,
Rigaku; thanks to IUCr for support and consultations.

\end{frame}

%------------------------------------------------------------------------------

\setbeamertemplate{footline}{
  \tiny
  \rule[-0.4\baselineskip]{0pt}{1.2\baselineskip}
  \hspace{1ex}
  {\em
    A path to freedom: 
    GNU $\rightarrow$
    Linux $\rightarrow$
    Ubuntu $\rightarrow$
    MySQL $\rightarrow$
    R $\rightarrow$
    \LaTeX $\rightarrow$
    TikZ $\rightarrow$
    Beamer
  }
}
  
\begin{frame}

  \centerline{\Large Thank you!}

  \vfill

  \begin{centering}
    %% \includegraphics[height=3cm]{images/Sphalerite-Quartz-261762.eps.gz}
      \begin{tabbing}
        \hspace{8mm} \=
        \includegraphics[width=4cm]{images/beryl-picture.eps.gz} \=
        \hspace{1cm} \=
        \includegraphics[width=5cm]{images/beryl-structure.eps.gz} \\
        \>
        \tiny
        \mywebref{http://en.wikipedia.org/wiki/Emerald} \> \>
        \tiny
        \mywebref{http://www.crystallography.net/5000095.html} \\
      \end{tabbing}
  \end{centering}

\end{frame}

%------------------------------------------------------------------------------

\begin{frame}
  \frametitle{References}

  \tiny
  %% \bibliographystyle{plain}
  \bibliographystyle{apalike}
  \bibliography{bibliography/citations}

\end{frame}

%------------------------------------------------------------------------------

\end{document}
