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index.html
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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Cytoscape App tutorial template</title>
<link rel="stylesheet" href="../../css/reveal.css">
<link rel="stylesheet" href="../../css/theme/cytoscape-protocol-1.css">
<!-- Theme used for syntax highlighting of code -->
<link rel="stylesheet" href="../../lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? '../../css/print/pdf.css' : '../../css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
</head>
<body>
<div class="reveal">
<div class="slides">
<!-- ========================================================== -->
<!-- THIS IS WHERE YOUR CONTENT BEGINS -->
<section>
<h1>App Tutorial Template</h1>
<p>This template introduces a core set of reveal.js components, a recommended style and useful tips for creating a tutorial protocol for your Cytoscape App.</p>
<p>Cytosape App tutorials are listed in a dedicated section of <a href="https://github.com/cytoscape/cytoscape-tutorials/wiki#cytoscape-apps" target="_blank">tutorials.cytoscape.org</a>. Check out these two examples of completed tutorials:</p>
<ul>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/" target="_blank">WikiPathways App Tutorial</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/" target="_blank">stringApp Tutorial</a></li>
</ul>
<!-- The footer is used to position an image with a hyperlink to the main tutorial site. It is left-aligned and the y-position is defined with the "style= "bottom:" " property. Default is -2m, but this has to be adjusted for each tutorial based on the other content on the slide. -->
<div class="footer" style="bottom: -3em;">
<a href="https://github.com/cytoscape/cytoscape-tutorials/wiki"><img class="plain" src="../../assets/images/cytoscape-tutorials.png" style="height:70px;opacity:0.5"></a></div>
</section>
<section>
<h1>Basics</h1>
<p>The reveal framework includes a large set of features and components. See links below for complete documentation.</p>
<ul>
<li><a href="https://github.com/cytoscape/cytoscape-tutorials/blob/gh-pages/README.md">Cytoscape Tutorials Using Reveal</a><ul style="list-style-type:none"><li><i>- Detailed information on all reveal components used for Cytoscape tutorials</i></li></ul></li>
<li><a href="https://github.com/cytoscape/cytoscape-tutorials/blob/gh-pages/reveal-readme.md">General reveal.js documentation</a><ul style="list-style-type:none"><li><i>- Complete documentation for the reveal framework</i></li></ul></li>
</ul>
<p>To get started, open <b>module.html</b> and <b>index.html</b> located in <b>protocols/module/template-app</b>. Review how <b>module.html</b> is pulled in from the <b>index.html</b> wrapper.</p>
</section>
<!-- The section tag defines one slide. The "highlight" tag is used for important text. -->
<section id='intro'>
<h1>Introduction</h1>
<p>Use the first slide to introduce your app and the tutorial content, including links to your <a href="http://apps.cytoscape.org/apps/wikipathways">tool</a>.</p>
<p>If you don't have a dedicated setup slide, any <highlight>specific installation instructions</highlight> can be included here.</p>
</section>
<!-- This slide shows the recommended use of bolding and higlighting -->
<section id='style'>
<h1>Recommended Style</h1>
<p>To help make the content as easy as possible to grasp, we are using highlighted and bold text as follows:</p>
<ul>
<li>Use the <highlight>highlight tag</highlight> for any actions you want the user to take. Example: "To open a session file, select <highlight>File → Open...</highlight>"</li>
<li>Use <b>bold</b> text for any other item you want to emphasize that is <b>not</b> an action. Example: "...data is visible in the <b>Node Table</b>".</li>
</ul>
</section>
<!--This is a slide with text in the form of a list, a figure and a citation -->
<section id='list-image-cit'>
<h1>List, Image and Citation</h1>
<p>Here, a bullet point list is used to introduce some features of the app, and a citation is provided.</p><br />
<!-- The figure is placed on the right side using "float:right" and is sized using "width"-->
<img style="float:right;width:45%" src="WP-App.png">
<ul style="width:45%">
<li>Search hundreds of pathways directly from Cytoscape</li>
<li>Import pathways as pathway or network</li>
<li>Visualize data or use for network analysis</li>
</ul>
<br />
<!--Citation is styled in a smaller font -->
<small style="margin-top:40px;">Kutmon (2014) WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. <em>F1000Res</em>, 2014 Jul 1</small>
</section>
<!--This is a slide with different styles of figures -->
<section id='list-image-styles'>
<h1>Image styles</h1>
<p>There are three different styles for images:</p><br />
<img class="plain" style="margin:15px;width:30%" src="WP-App_plain.png">
<img class="border" style="margin:15px;width:30%" src="WP-App_border.png">
<img style="margin:15px;width:30%" src="WP-App.png">
</section>
<!-- This is a slide with two-column layout -->
<section id='two-columns'>
<h1>Two-column slide layout</h1>
<p>The two-column slide layout is convenient for placing text. This example shows two lists of URLs.</p>
<div class="column">
<h5><highlight>Cancer pathways</highlight></h5>
<ul>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP4262">Breast cancer pathway</a></li>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP4239">EMT in colon cancer</a></li>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP3972">PDGFR-beta pathway</a></li>
</ul>
</div>
<div class="column">
<h5><highlight>Disease pathways</highlight></h5>
<ul>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP3569">Fanconi Anemia Pathway</a></li>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP2059">Alzheimers Disease</a></li>
<li><a href="https://www.wikipathways.org/index.php/Pathway:WP2447">Amyotrophic lateral sclerosis</a></li>
</ul>
</div>
</section>
<!-- This is a slide with animation -->
<section id='frag-list'>
<h1>Animated List Elements</h1>
<p>Here's an example of an animated list. Click the down or right arrow to step through the list.</p><br />
<h5><highlight>WikiPathways App Features</highlight></h5>
<ul>
<li>Search hundreds of pathways directly from Cytoscape</li>
<li class="fragment">25 species represented</li>
<li class="fragment">Import pathways as pathway or network</li>
<li class="fragment">Visualize data or use for network analysis</li>
</ul>
</section>
<!-- THIS IS WHERE YOUR CONTENT ENDS -->
<!-- ========================================================== -->
</div>
</div>
<script src="../../lib/js/head.min.js"></script>
<script src="../../js/reveal.js"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-155159-15', 'auto');
ga('send', 'pageview');
</script>
<script>
Reveal.addEventListener( 'ready', function() {
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<script>
// More info https://github.com/hakimel/reveal.js#configuration
Reveal.initialize({
history: true,
controls: true,
progress: true,
slideNumber: false,
touch: true,
fragments: true,
help: true,
showNotes: false,
previewLinks: false,
transition: 'slide', // none/fade/slide/convex/concave/zoom
width: 1200,
height: 860,
autoSlide: 0,
// More info https://github.com/hakimel/reveal.js#dependencies
dependencies: [
{ src: '../../plugin/markdown/marked.js' },
{ src: '../../plugin/markdown/markdown.js' },
{ src: '../../plugin/zoom-js/zoom.js', async: true, condition: function(){ return !!document.body.classList; } },
{ src: '../../plugin/notes/notes.js', async: true },
{ src: '../../plugin/highlight/highlight.js', async: true, callback: function() { hljs.initHighlightingOnLoad(); } },
{ src: '../../plugin/external/external.js', condition: function() { return !!document.querySelector( '[data-external]' ); } }
]
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</body>
</html>