diff --git a/beamer_embl.tex b/beamer_embl.tex deleted file mode 120000 index 97f38d83f35dca5065e0d663a7b170bbad6594f1..0000000000000000000000000000000000000000 --- a/beamer_embl.tex +++ /dev/null @@ -1 +0,0 @@ -../Dokumentumok/pw/slides/beamer_embl.tex \ No newline at end of file diff --git a/beamer_embl.tex b/beamer_embl.tex new file mode 100644 index 0000000000000000000000000000000000000000..b99781c0b972d0b3bfbad7c903a4acd7b6dd7099 --- /dev/null +++ b/beamer_embl.tex @@ -0,0 +1,272 @@ +% % % % % % % % % % % % % % % % % % % % % % % % % +% +% EMBL(-EBI) style template for XeLaTeX Beamer +% +% Copyright (c) 2014-2015 - EMBL-EBI +% +% File author(s): Dénes Türei (denes@ebi.ac.uk) +% +% Distributed under the GPLv3 License. +% See accompanying file LICENSE or a copy at +% http://www.gnu.org/licenses/gpl-3.0.html +% +% Website: http://www.ebi.ac.uk/~denes +% +% This template has been made according to the +% EMBL style guidelines. +% Please see the URLs below for more details. +% +% http://intranet.ebi.ac.uk/sites/intranet.ebi.ac.uk/files/content/outreach/EMBL_branding_guidelines.pdf +% http://intranet.ebi.ac.uk/outreach/writing-embl-style-guide +% +% Tested with XeTeX, Version 3.14159265-2.6-0.99991 +% (TeX Live 2014/Arch Linux) +% +% % % % % % % % % % % % % % % % % % % % % % % % % + +\documentclass[aspectratio=1610]{beamer} % this is for 16:10 wide screens + % set this according to the actual presentation room + +% XeLaTeX packages +\usepackage[no-math]{fontspec} +\usepackage{xunicode} +\usepackage{polyglossia} +\setdefaultlanguage{english} +\usepackage{xltxtra} +\usepackage{adjustbox} +\usepackage{beamerthemesplit} +\usepackage{natbib} +\usepackage{upgreek} + +% 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{emblgray1}{gray}{0.875} +\definecolor{emblgray8}{gray}{0.125} +\definecolor{emblgray75}{gray}{0.25} + +% Beamer theme settings +\setbeamercovered{transparent} +\mode +{ \usetheme{PaloAlto} + \setbeamercolor{normal text}{fg=emblgray75,bg=white} + \usecolortheme[named=emblpetrol]{structure} + \setbeamercolor{logo}{bg=emblgreen} + \useinnertheme{circles} + \usefonttheme[onlymath]{serif} + \setbeamercovered{transparent} + \setbeamertemplate{blocks}[rounded][shadow=true] + \setbeamercolor{section in sidebar}{fg=white} %color of the active section + \setbeamercolor{section in sidebar shaded}{fg=emblgray1} +} + +\defaultfontfeatures{Mapping=tex-text} + +% we don't need all of these all the time +\usepackage{graphicx} +\usepackage{tikz} +\usepackage{xcolor,color} +\usepackage{booktabs} +\usepackage{hyperref} + +\usepackage{units} +\usepackage{fouridx} +\usepackage{tabularx} +\usepackage{multicol} +\usepackage{chngcntr} + +% Figure numbering +%\counterwithout{figure}{section} +\counterwithin{figure}{section} + +\usetikzlibrary{positioning,shapes,shadows,calc,arrows} + +\pgfdeclarelayer{edges} % declare background layer +\pgfdeclarelayer{groups} +\pgfsetlayers{groups,edges,main} + +\newcommand{\ptitle}[1]{ + \begin{center} + \begin{tikzpicture} + \node[ptitle] at (0,0) {#1}; + \end{tikzpicture} + \end{center} +} + +% EMBL official fonts are Helvetica Neue from Linotype and Sentinel from Hoefler & Frere Jones +\setmainfont{Sentinel-Book} +\newfontface{\sentinelitalic}[Path=fonts/]{Sentinel-BookItalic.otf} +\newfontface{\sentinelbold}[Path=fonts/]{Sentinel-Bold.otf} +\newfontface{\sentinelsemibold}[Path=fonts/]{Sentinel-Semibold.otf} +\setsansfont[LetterSpace=3]{HelveticaNeueLTStd-Lt} +% + +\color{black} + +% recently in english typography also french spacing is preferred +\frenchspacing + +% here you can put anything what will appear in the left top corner green square: +\logo{} + +% fake hungarian umlauts +\def\huu{u\hspace*{-0.43em}\symbol{\string"02DD}\hspace*{-0.07em}} +\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} +% or if you compile the document on the day of your presentation: +% \date{\today} +% optionally, your email: +%\\{\footnotesize turei.denes@gmail.com} + + +% % % % % % % % % % +\begin{document} % +% % % % % % % % % % + + +\newcounter{thepic} \setcounter{thepic}{1} +% % % % % +\frame{\titlepage \vspace{-0.5cm}} + + +% new section +\section{Intro} + +% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % +% sample slides (titles, subtitles, itemize, placement with tikz, etc.) % +% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % + +\begin{frame}{Signaling networks and pathways} + + + \begin{tikzpicture} + \node[anchor=north west] at (0.6,0) { + \begin{minipage}{0.75\textwidth} + {\color{emblgreen} Interactomes vs. pathways}\\ + \begin{itemize} + \item PPI network: binary interactions + \item Pathways: directions, signs $=$ causality + \item High vs. low throughput experiments + \item Literature curation + \end{itemize} + + \vspace*{0.66\baselineskip} + High quality $\Longleftrightarrow$ high coverage\vspace*{0.33\baselineskip}\\ + + {\color{emblgreen} Criticism}\\ + \begin{itemize} + \item Curation mistakes + \item Research bias + \end{itemize} + \end{minipage}}; + \node[anchor=north east] at (0,0) {\includegraphics[width=0.33\textwidth]{pathway.pdf}}; + \end{tikzpicture} +\end{frame} + +\begin{frame}{Objectives} + + {\color{emblgreen}\Large Signalling network} + \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 + \end{itemize} + {\color{emblgreen}\Large Software} + \begin{itemize} + \item Python modules + \end{itemize} + {\color{emblgreen}\Large Possible applications} + \begin{itemize} + \item Modeling + \item Graph topology and dynamics + \end{itemize} +\end{frame} + +\begin{frame}{} + \begin{center} + %\includegraphics[width=0.4\textwidth]{kirouac_hmap.png} + \end{center} + \begin{flushright} + Edge consistency \textbullet\ from Kirouac et al. 2012 + \end{flushright} +\end{frame} + +\section{Pathways} +\begin{frame}{Resources: content} + \vspace*{-1ex} + %\includegraphics[width=\textwidth]{../a2/src/results/databases-clpce.pdf} +\end{frame} + +\begin{frame}{Pathway resources} + + \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\\ + \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} +\end{frame} + +\begin{frame}{Coverage} + + + {\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 +\end{frame} + +\section{Alternatives} +\begin{frame}{Alternatives: PathwayCommons, ConsensusPathDB} + + {\color{emblgreen}\Large PathwayCommons} \hfill {\color{emblpetrol}\footnotesize\textbullet\ http://pathwaycommons.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 + \end{itemize} +\end{frame} + +\section{} +\begin{frame}{Acknowledgements} + + {\color{emblgreen}\Large Systems Biomedicine Group, EMBL-EBI, Hinxton}\\ + \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} + \end{itemize} + {\color{emblgreen}\Large EIPOD fellowship}\\ + \begin{itemize} + \item John Overington (ChEMBL Group, EMBL-EBI, Hinxton) + \item Anne-Claude Gavin (Biomolecular Networks Group, EMBL Heidelberg) + \end{itemize} + Tamas Korcsmaros (TGAC \& IFR, Norwich)\\ + NetBiol Group, Eotvos University, Budapest, Hungary\\ + Link Group, Semmelweis University, Budapest, Hungary\\ +\end{frame} + +\end{document} \ No newline at end of file diff --git a/embl.gpl b/embl.gpl deleted file mode 120000 index 4478b13c5531ce935b0e1a0f35c1d739072813cf..0000000000000000000000000000000000000000 --- a/embl.gpl +++ /dev/null @@ -1 +0,0 @@ -../Dokumentumok/embl.gpl \ No newline at end of file diff --git a/embl.gpl b/embl.gpl new file mode 100644 index 0000000000000000000000000000000000000000..bf7c57831d6b65ed800eea4dc887ed88a18df5cd --- /dev/null +++ b/embl.gpl @@ -0,0 +1,40 @@ +GIMP Palette +Name: embl.gpl +Columns: 1 +# +110 169 69 Mantis +132 180 92 Feijoa +151 190 115 Chelsea cucumber +169 201 139 Madang +205 223 187 Pale leaf +223 234 210 Willow brook +239 244 233 Twilight blue +0 123 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