Commit 7826a40f authored by Türei Dénes's avatar Türei Dénes

filled with suggestions and blind text

parent 36eeae62
File added
......@@ -37,12 +37,14 @@
\usepackage{beamerthemesplit}
\usepackage{natbib}
\usepackage{upgreek}
\usepackage{blindtext}
% EMBL colors
\definecolor{emblpetrol}{RGB}{0, 102, 102}
\definecolor{emblgreen}{RGB}{115, 179, 96}
\definecolor{emblyellow}{RGB}{250, 183, 0}
\definecolor{emblred}{RGB}{227, 62, 62}
\definecolor{emblbrown}{RGB}{153, 106, 68}
\definecolor{emblgray1}{gray}{0.875}
\definecolor{emblgray8}{gray}{0.125}
\definecolor{emblgray75}{gray}{0.25}
......@@ -116,14 +118,22 @@
\def\huo{o\hspace*{-0.46em}\symbol{\string"02DD}\hspace*{0.03em}}
% here you set short title, full title, your name(s), institute, and other affiliations, and the date
\title[Literature curated pathways]{Pathways: causality and mechanisms behind patterns. Resources, methods, applications}
\author{Denes Turei}
\institute{\begin{tiny}Saez-Rodriguez group (EMBL Hinxton)\par Overington group (EMBL Hinxton)\par Gavin group (EMBL Heidelberg)\par\end{tiny}\vspace*{\baselineskip} EMBL-EBI\hspace*{0.247em}\raisebox{-1.21ex}{\includegraphics[height=3.80ex]{embl1.pdf}} }
\date{4th June 2015}
\title[Short title]{An awesome title, only for the title slide, no matter if very long}
\author{Your Name}
\institute{\begin{tiny}Your Group (EMBL Heidelberg)\par Other Group (EMBL-EBI Hinxton)\par Another Group (EMBL Monterotondo)\par\end{tiny}\vspace*{\baselineskip} EMBL\hspace*{0.247em}\raisebox{-1.21ex}{\includegraphics[height=3.80ex]{embl1.pdf}} }
\date{21st March 2017
% or if you compile the document on the day of your presentation:
% \date{\today}
% optionally, your email:
%\\{\footnotesize turei.denes@gmail.com}
\\{\footnotesize your.name@embl.de}
}
\addtobeamertemplate{navigation symbols}{}{%
\usebeamerfont{footline}%
\usebeamercolor[fg]{footline}%
\hspace{1em}%
\raisebox{0.4ex}{[ \insertframenumber\ / \inserttotalframenumber\ ]}
}
% % % % % % % % % %
......@@ -143,130 +153,135 @@
% sample slides (titles, subtitles, itemize, placement with tikz, etc.) %
% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % %
\begin{frame}{Signaling networks and pathways}
\begin{frame}{This below is embedded into a tikzpicture}
\begin{tikzpicture}
\node[anchor=north west] at (0.6,0) {
\begin{minipage}{0.75\textwidth}
{\color{emblgreen} Interactomes vs. pathways}\\
{\color{emblgreen} Official fonts\ldots}\\
\begin{itemize}
\item PPI network: binary interactions
\item Pathways: directions, signs $=$ causality
\item High vs. low throughput experiments
\item Literature curation
\item \ldots of EMBL are
\item Helvetica Neue from Linotype
\item \textrm{Sentinel from Hoefler \& Frere Jones}
\item of Helvetica Neue the light is most often used
\end{itemize}
\vspace*{0.66\baselineskip}
High quality $\Longleftrightarrow$ high coverage\vspace*{0.33\baselineskip}\\
This $\Longleftrightarrow$ and that\vspace*{0.33\baselineskip}\\
{\color{emblgreen} Criticism}\\
{\color{emblgreen} These are not free for anyone}\\
\begin{itemize}
\item Curation mistakes
\item Research bias
\item But EMBL has licensed them
\item You can {\color{emblpetrol}\href{http://intranet.ebi.ac.uk/outreach/writing-embl-style-guide}{access them here}}
\end{itemize}
\end{minipage}};
%\node[anchor=north east] at (0,0) {\includegraphics[width=0.33\textwidth]{pathway.pdf}};
% this whole thing makes sense if you want to place some small illustration on the margin:
%\node[anchor=north east] at (0,0) {\includegraphics[width=0.33\textwidth]{something.pdf}};
\end{tikzpicture}
\end{frame}
\begin{frame}{Objectives}
\begin{frame}{Larger green titles}
{\color{emblgreen}\Large Signalling network}
{\color{emblgreen}\Large Check the canvas}
\begin{itemize}
\item High quality pathways
\item Manually curated, from low-throughput studies
\item Directed and signed edges where it's possible
\item Structural and functional annotations
\item 3:4 or 10:16 aspect ratio
\item Find out about the room where you will present
\item Test the computer connection
\item VGA sometimes transmits only 1024$\,\times\,$768
\item Solution: have a HDMI cable with you
\end{itemize}
{\color{emblgreen}\Large Software}
\begin{itemize}
\item Python modules
\end{itemize}
{\color{emblgreen}\Large Possible applications}
{\color{emblgreen}\Large From now}
\begin{itemize}
\item Modeling
\item Graph topology and dynamics
\item I show some blind text
\item Just to fill the space
\end{itemize}
{\color{emblgreen}\Large Nice green}
\blinditemize[2]
\end{frame}
\begin{frame}{}
\begin{frame}{Picture example}
\begin{center}
%\includegraphics[width=0.4\textwidth]{kirouac_hmap.png}
%\includegraphics[width=0.4\textwidth]{hmap.png}
\end{center}
\begin{flushright}
Edge consistency \textbullet\ from Kirouac et al. 2012
An example how to include a picture with centering (edit the file name and comment out) \textbullet\ from Johnson et al. 2012
\end{flushright}
\end{frame}
\section{Pathways}
\begin{frame}{Resources: content}
%
\section{Graphics}
%
\begin{frame}{Graphics adjusted to full width}
\vspace*{-1ex}
%\includegraphics[width=\textwidth]{../a2/src/results/databases-clpce.pdf}
%\includegraphics[width=\textwidth]{../a2/src/results/a3.pdf}
\end{frame}
\begin{frame}{Pathway resources}
\begin{frame}{A nice box}
\begin{block}{Resources (27)}
{\color{emblgreen} Directed} (13)\\
ARN, CA1, DEPOD, DOMINO, Guide2Pharmacology, HPRD, Macrophage, NCI-PID, NRF2ome, PDZBase, PhosphoSite, SPIKE, SignaLink2, Signor, dbPTM, phosphoELM\\
{\color{emblgreen} Non-directed} (11)\\
AlzPathway, CancerCellMap, DIP, DOMINO, DeathDomain, ELM, InnateDB, IntAct, MPPI, MatrixDB, NetPath\\
\begin{block}{Cool box, wow!}
{\color{emblgreen} This box comes from\ldots} (13)\\
The original Palo Alto template\\
{\color{emblgreen} Something else} (11)\\
Bla bla blah\\
\end{block}
\begin{itemize}
\item Size (giant component): 7,088 nodes, 35,147 edges
\item 21,294 PubMed IDs
\item 20,738 directed edges
\item Diameter: 12, mean degree: 9.74
\item Directions, signs
\item Various annotations (localization, role, etc)
\end{itemize}
\blindenumerate[5]
% \begin{itemize}
% \item
% \end{itemize}
\end{frame}
\begin{frame}{Coverage}
%
\section{Colors}
%
\begin{frame}{Colors of EMBL}
{\color{emblgreen}\textasciitilde30$\,$\% of the human proteome}\par
{\color{emblred}\textasciitilde80$\,$\% of the cancer dirvers and drug targets}\par
{\color{emblyellow}\textasciitilde20$\,$\% of proteins have known compounds}\par
{\color{emblgray75}\textasciitilde90$\,$\% of proteins are in proteomics datasets}\par
{\color{emblpetrol}\textasciitilde30$\,$\% petrol (teal)}\par
{\color{emblgreen}\textasciitilde30$\,$\% green (mantis)}\par
{\color{emblred}\textasciitilde80$\,$\% red (crimson)}\par
{\color{emblyellow}\textasciitilde20$\,$\% gold}\par
{\color{emblgray75}\textasciitilde90$\,$\% gray}\par
{\color{emblbrown}\textasciitilde4$\,$\% brown}\par
\ldots each of these colors except brown has 7 shades, this makes a total of 35 colors. The brown is not an official EMBL color but used on the webpage. See the palette in embl.gpl.\par
\end{frame}
\section{Alternatives}
\begin{frame}{Alternatives: PathwayCommons, ConsensusPathDB}
\begin{frame}{Titles with labels}
{\color{emblgreen}\Large PathwayCommons} \hfill {\color{emblpetrol}\footnotesize\textbullet\ http://pathwaycommons.org/}
{\color{emblgreen}\Large Something} \hfill {\color{emblpetrol}\footnotesize\textbullet\ \href{http://something.org/}{http://something.org/}}
\begin{itemize}
\item 18 resources {\footnotesize – only IntAct in common with my network}
\item Vast amount of HTP data
\item References and evidences only in BioPax format
\item R package: Paxtools
\end{itemize}
{\color{emblgreen}\Large ConsensusPathDB} \hfill {\color{emblpetrol}\footnotesize\textbullet\ http://consensuspathdb.org/}
\begin{itemize}
\item 15 resources {\footnotesize – 6 also in my network}
\item Not only direct physical and biochemical interactions
\item Clear references
\item Web based gene set analysis
\item The dark green labels {\footnotesize – are adjusted to the right}
\item
\item
\item
\end{itemize}
{\color{emblgreen}\Large Another thing} \hfill {\color{emblpetrol}\footnotesize\textbullet\ \href{http://anotherthing.org/}{http://anotherthing.org/}}
% \begin{itemize}
% \item
% \end{itemize}
\blinditemize[4]
\end{frame}
%
\section{}
%
\begin{frame}{Acknowledgements}
{\color{emblgreen}\Large Systems Biomedicine Group, EMBL-EBI, Hinxton}\\
{\color{emblgreen}\Large Your Group, EMBL Heidelberg}\\
\begin{itemize}
\item Julio Saez-Rodriguez\\
\item {\footnotesize Luz Garcia Alonso, Thomas Cokelaer, Lekshmi Dharmarajan, Federica Eduati, Marti Bernardo Faura, Emanuel Gonçalves,Francesco Iorio, Angeliki Kalamara, Victoria Doldan Martelli, Michael Schubert, Michael Menden}
\item Your Team Leader?\\
\item {\footnotesize Please note, here we started an untitled section, so no section is highlighted on the left bar}
\end{itemize}
{\color{emblgreen}\Large EIPOD fellowship}\\
{\color{emblgreen}\Large You Collaborators}\\
\begin{itemize}
\item John Overington (ChEMBL Group, EMBL-EBI, Hinxton)
\item Anne-Claude Gavin (Biomolecular Networks Group, EMBL Heidelberg)
\item AB (Group)
\item XY (Lab)
\end{itemize}
Tamas Korcsmaros (TGAC \& IFR, Norwich)\\
NetBiol Group, Eotvos University, Budapest, Hungary\\
Link Group, Semmelweis University, Budapest, Hungary\\
Other Collaborator (Some Institure, Norwich)\\
Another University, Novosibirsk, Russia\\
\end{frame}
\end{document}
\ No newline at end of file
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