phd-defence-fr/introduction.tex

\begin{frame}{Le projet ANR SynBioTIC (2011—2015)}
  \framesubtitle{Biologie synthétique}

  \begin{columns}
    \column{.6\textwidth}
    \begin{itemize}
      % Abstraction, Découplage, Composition (ingénierie)
      \item \structure{Biologie synthétique}
        \begin{itemize}
          \item Génie génétique \\
            Production d'insuline par \structure{une} bactérie\\
            \structure{[Riggs et Itakura, 1978]}
          \item \structure{Abstraction}, standardisation, découplage 
        \end{itemize}
        \medskip
      \item Projet exploratoire:
        « permettre l'exploitation des \structure{propriétés collectives} d'une
        population bactérienne pour créer des biosystèmes artificiels.»\\
        \medskip
    \end{itemize}

    \column{.3\textwidth}
    \centering
    \tourdelangages[white][white][white]
    \tikz[overlay,abs/.style={ultra thick,-Stealth,thick,transform canvas={xshift=2mm}}]
    \draw[abs] (genotype.east) to node[anchor=base,rotate=-90,yshift=1mm] {abstraction} (population.east);
  \end{columns}
\end{frame}

%\newsavebox{\haskellfib}
%\begin{lrbox}{\haskellfib}
%\end{lrbox}
%\usebox{\haskellfib}

\begin{frame}[fragile]{Problématique}
  \framesubtitle{compilation et multi-niveau}

  \centering
  \begin{tikzpicture}[%
    node distance=15mm,
    wp/.style={draw},%
    compilation/.style={compilcol,line width=5mm,-Triangle Cap},
    emergence/.style={alert,thick,-Stealth,decorate,decoration={snake,
      amplitude=.5mm,segment length=2mm,post length=2mm}}]
      \uncover<2-> {
        \node[wp] (ibn) {%
            \begin{tikzpicture}
              \clip (0cm,0cm) rectangle (3cm,2cm);
              \node[anchor=center,yshift=-9mm] at (15mm,1cm) {%
                \includegraphics[width=3cm]{vector/binary}};
            \end{tikzpicture}
          };
      }
      \begin{onlyenv}<2->
        \node[wp,above=of ibn] (ihn) {%
            \begin{tikzpicture}
              \clip (0cm,0cm) rectangle (3cm,2cm);
              \node[anchor=center,text width=3cm] at (15mm,1cm) {%
                  \small
                  \lstset{style=haskell}
                  \begin{lstlisting}
fib 0 = 0
fib 1 = 1
fib n = fib (n-1)
      + fib (n-2)
                  \end{lstlisting}
                };
              \node[anchor=center,minimum width=3cm, minimum height=2cm,fill=white,
                opacity=0.9] at (15mm,1cm){\fontsize{55pt}{0}$f$};
            \end{tikzpicture}%
          };
        \draw[compilation] (ihn) to node[auto] {Compilation} (ibn);
      \end{onlyenv}
      \node[wp,right=3cm of ibn,label=below:{\small Niveau local}] (bbn) {%
          \begin{tikzpicture}
            \clip (0cm,0cm) rectangle (3cm,2cm);
            \node[anchor=center,yshift=9mm] at (15mm,1cm) {%
              \includegraphics[height=37mm]{vector/ecolihelix}};
          \end{tikzpicture}
        };
      \node[wp,above=of bbn,label=above:{\small Niveau global}] (bhn) {%
          \begin{tikzpicture}
            \clip (0cm,0cm) rectangle (3cm,2cm);
            \node[anchor=center] at (15mm,1cm) {%
              \includegraphics[width=3cm]{vector/petri}};
          \end{tikzpicture}
        };
      \draw[emergence,transform canvas={xshift=-1cm}] (bbn) to (bhn);%
      \draw[emergence,transform canvas={xshift=1cm}] (bbn) to (bhn);%
      \visible<1-2>{
        \draw[emergence] (bbn) to node[black,fill=white,opacity=.8]
        {émergence} (bhn);
      }%
      \visible<3>{
        \draw[compilation] (bhn) to (bbn);
      }
      \uncover<2->{
        \node[right=4mm of ihn,text width=2cm, align=center]
        {\small Haut niveau\\ de description};
        \node[right=4mm of ibn,text width=2cm, align=center]
        {\small Bas niveau\\ de description};
      }
  \end{tikzpicture}

\end{frame}

\begin{frame}%[label=this one]
  \frametitle{Le projet ANR \textsc{SynBioTIC} (2011—2015)}

  \begin{columns}
    \column{.8\textwidth}
    \begin{itemize}
      \item Découpe en work-package
        \begin{itemize}
          \item \textcolor{black!40}{WP1: Études des formes, fourni des exemples}
          \item \structure<2>{WP2: Programmation spatiale (L1)}
          \item \structure<2>{WP3: Programmation orienté entité (L2)}
          \item WP4: Réseau de régulation génétique (L3)
          \item \textcolor{black!40}{WP5: Calculabilité}
          \item \textcolor{black!40}{WP6: Sûreté, sécurité}
        \end{itemize}
    \end{itemize}

    \column{.2\textwidth}
    \centering
    \tourdelangages[white][white][white][compilcol]
    \begin{tikzpicture}[overlay,
      wp/.style={draw,text width=2cm,font=\footnotesize,align=center,
      minimum width=22mm, minimum height=12mm},
      ]
      %\path (population) to node[auto,xshift=-2mm,swap] {Compilation} (phenotype);
      %\path (phenotype)  to node[auto,xshift=-2mm,swap] {Compilation} (genotype);
      \uncover<2>{
        \node[structure,left=1mm of population] {L1};
        \node[structure,left=1mm of phenotype]  {L2};
        \node[left=1mm of genotype]   {L3};
      }
    \end{tikzpicture}
  \end{columns}
\end{frame}