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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Welcome to Cytoscape 3</title>
<meta name="description" content="Introduction to Cytoscape 3.">
<meta name="author" content="Keiichiro Ono">
<link href="css/main.css" rel="stylesheet" media="screen"/>
<link href="css/slides.css" rel="stylesheet" media="screen"/>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js"></script>
<script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.10.2/jquery-ui.min.js"></script>
<script src="js/global_variables.js"></script>
<script src="js/menu_generator.js"></script>
<script src="js/slides.min.jquery.js"></script>
<script>
$(function () {
// Set starting slide to 1
var startSlide = 1;
// Get slide number if it exists
if (window.location.hash) {
startSlide = window.location.hash.replace('#', '');
}
// Initialize Slides
$('#slides').slides({
preload: true,
preloadImage: 'images/slides/loading.gif',
generatePagination: true,
play: 5000,
pause: 2500,
hoverPause: true,
// Get the starting slide
start: startSlide,
animationComplete: function (current) {
// Set the slide number as a hash
window.location.hash = '#' + current;
}
});
});
</script>
</head>
<body>
<div id="container">
<script src="js/header.js"></script>
<div id="documents">
<div class="blockfull3">
<div id="container2">
<div id="example">
<div id="slides">
<div class="slides_container">
<div class="slide">
<div class="text">
<h1>Welcome!</h1>
<p>
Cytoscape 3.0 is a cleaner and modular new generation
of Cytoscape for future expansions. It benefits both
users and developers.
</p>
</div>
<a href="images/slides/title0.png" title="Cytoscape 3 Desktop Version">
<img src="images/slides/title0.png" alt="Cytoscape 3 Desktop"/>
</a>
</div>
<div class="slide">
<div class="text">
<h1>New Features</h1>
<p>
Cytoscape 3 has new features including: <strong>Edge Bundling,
Network Collections, Visual Annotations, Advanced Search,
and Improved Data Table Browser</strong>.
</p>
<p>
<a href="release_notes_3_0_1.html">Learn more about new features ›</a>
</p>
</div>
<a href="images/slides/new_features.png" title="New Features">
<img src="images/slides/new_features.png"/>
</a>
</div>
<div class="slide">
<div class="text">
<h1>App Store</h1>
<p>
You can install Apps directly from Cytoscape App Store.
</p>
<p>
<a href="http://apps.cytoscape.org/">Visit Cytoscape App Store ›</a>
</p>
</div>
<a href="images/slides/appstore.png" title="App Store">
<img src="images/slides/appstore.png"/>
</a>
</div>
</div>
</div>
<div id="frame"></div>
</div>
</div>
<div class="textleft">
<ul>
<li>
<a href="download.php">
<button class="button hugerounded orange">
Download Cytoscape 3.0
</button>
</a>
</li>
<li>
<a href="cy3_welcome_letter_v8.pdf">
<button class="button hugenarrow green">
Download Welcome Letter
</button>
</a>
</li>
<li>
<a href="manual/Cytoscape3_0_1Manual.pdf">
<button class="button hugenarrow blue">
User Manual
</button>
</a>
</li>
<li>
<a href="release_notes_3_0_1.html">
<button class="button hugenarrow blue">
Release Notes
</button>
</a>
</li>
<li>
<a href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3">
<button class="button hugenarrow blue">
Tutorials
</button>
</a>
</li>
</ul>
</div>
</div>
</div>
<div class="blockfull3">
<h2>What is Cytoscape 3.0?</h2>
<div class="rightimg">
<img src="images/cytoscape_logo_left.png"/>
</div>
<div class="section">
Cytoscape 3.0 is the latest version of Cytoscape, which introduces a whole new architecture,
developer API and set of user controls. Cytoscape 3.0 represents a major redesign from the
ground up, toward the goal of provide a stable, extensible, high-performance platform for
network visualization and analysis. The initial Beta Release will introduce users to the new
interfaces and features we've been working on:
<ul>
<li>
New welcome screen and toolbar for quick access to common actions
</li>
<li>
New Data Table controls to interface with your data
</li>
<li>
Integrated support for graphical annotations in networks
</li>
<li>
Support for independent sets of networks within a single session
</li>
<li>
Advanced network and table import controls
</li>
<li>
Improved architecture and API for a more stable experience
</li>
<li>
Cut/Copy/Paste of nodes and edges
</li>
<li>
Metanode support in the core
</li>
<li>
Context menus for improved usability
</li>
</ul>
</div>
<h2>Apps for Cytoscape 3.0</h2>
<div class="section">
You can install Cytoscape 3 Apps directly from new Cytoscape App Store. Please
visit <a href="http://apps.cytoscape.org/" target="_new">apps.cytoscape.org</a>.
</div>
<h2>Report Bugs</h2>
<div class="textright">
<a href="http://chianti.ucsd.edu/cyto_web/bugreport/bugreport.php">
<button class="button hugenarrow red">
Report a Bug
</button>
</a>
</div>
<div class="section">
We need your help to improve quality of Cytoscape 3. You can report a bug from
<strong>Help → Report a Bug...</strong>. Or, click this button:
</div>
<h2>Developer Documents</h2>
<div class="section">
Cytoscape 3 is an open-source platform and source code is hosted on Github.
<ul>
<li>
<a href="https://github.com/cytoscape">Cytoscape source code on Github</a>
</li>
<li>
<a href="http://chianti.ucsd.edu/cytoscape-3.0.1/API">Cytoscape API 3.0.1 JavaDocs</a>
</li>
<li>
<a href="http://chianti.ucsd.edu/cytoscape-3.0.1/API.zip">3.0.1 API JavaDocs file (zipped)</a>
</li>
<li>
<a href="http://chianti.ucsd.edu/cytoscape-3.0.1/cytoscape-swing-app-api-3.0.1.jar">API JAR 3.0.1</a>
</li>
<li>
<a href="https://github.com/cytoscape/cytoscape-gui-distribution/tree/3.0.1">App Developer Project Tag</a>
</li>
<li>
Primary documentation for Cytoscape 3.0
<a href="http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper">app development</a>.
</li>
<li>
<a href="http://code.cytoscape.org/">Cytoscape Core Developer Portal (code.cytoscape.org)</a>
</li>
<li>
Learn about the <a href="http://wiki.cytoscape.org/Cytoscape_3/CoreDevelopment">Architecture,
Backward Compatibility,
and API</a> of Cytoscape 3.0.
</li>
<li>
All Cytoscape 3.0 <a href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3">app
development tutorials</a>.
</li>
</ul>
</div>
</div>
<script src="js/footer.js"></script>
</div>
</body>
</html>