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release_notes_3_0_0_beta.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link href="css/main.css" type="text/css" rel="stylesheet"
media="screen">
<title>Cytoscape 3 Beta 1 Release Notes</title>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.1/jquery-ui.min.js"></script>
<script type="text/javascript" src="js/global_variables.js"></script>
<script type="text/javascript" src="js/menu_generator.js"></script>
</head>
<body>
<div id="container">
<script src="js/header.js"></script>
<div id="documents">
<div class="blockfull3">
<h1>Cytoscape 3.0.0 Beta 1 Release Notes</h1>
<img src="images/cytoscape3_release_beta1.png" />
<h2>New Features in Cytoscape 3</h2>
<div class="section">
<h3>Welcome Screen</h3>
<div class="leftimg">
<img src="images/welcome_screen.png" />
</div>
<p>
For convenience, Cytoscape shows <strong><i>Welcome Screen</i></strong> at startup timewhich provides easy way to access
sample data sets and public databases.
</p>
</div>
<div class="section">
<h3>Edge Bend Visual Property</h3>
<div class="leftimg">
<img src="images/edge_bend_editor.png" />
</div>
<p>
Edge Bend is now a standard Visual Property. You can use it as a part of your Visual Style.
</p>
</div>
<div class="section">
<h3>Edge Bundling</h3>
<img src="images/edge_bundling.png" />
<p>
You can bundle edges by automatic Edge Bundling. This feature is useful for dense network views.
</p>
</div>
<div class="section">
<h3>Network Annotations</h3>
<div class="rightimg">
<img src="images/network_annotation.png" />
</div>
<p>
You can add notes and simple shapes to background or foreground of network view.
</p>
</div>
<div class="section">
<h3>Advanced Search Function</h3>
<div class="rightimg">
<img src="images/advanced_search.png" />
</div>
<p>
From this version, EnhancedSearch plugin is part of core. You can search networks using Lucene syntax.
</p>
</div>
<div class="section">
<h3>Show All feature in Data Table Browser</h3>
<div class="rightimg">
<img src="images/table_browser.png" />
</div>
<p>
By selecting <i>Show All</i> option in Data Table Browser, you can display all network objects in the
table. Nodes and edges will be selected when you select associated rows in the table.
</p>
</div>
<div class="section">
<h3>Network Collection</h3>
<div class="rightimg">
<img src="images/network_collection.png" />
</div>
<p>
Cytoscape 3 manages networks based on Network Collection. When you load networks to Cytoscape,
you can choose creating a new set of networks or adding them to existing collection.
</p>
</div>
<h2>User Manual</h2>
<div class="section">
<p>
User manual for Cytoscape 3 is available
<a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual">here</a>.
</p>
</div>
<h2>Known Issues</h2>
<div class="section">
<h3>Java Versions</h3>
<p>
You can run Cytoscape 3 on Java 6 or 7. However, there are several problems if you use
OpenJDK. Please use Oracle JRE/JDK or Apple Java Virtual Machine.
</p>
<h3>Important Note for Mac Users</h3>
<p>
If you run Cytoscape on Mac OS X 10.7.5+ and 10.8+, you need to disable Gatekeeper
before running the installer.
</p>
</div>
<h2>How to Report Bugs</h2>
<div class="section">
<p>
This version of Cytoscape is still in beta status and your bug reports are very important
to improve the quality of final version of Cytoscape 3. If you notice any problems,
please report them from:
<h3>Help → Report a bug...</h3>
</p>
</div>
<h2>Need Help?</h2>
<div class="section">
<p>
We need your feedback to improve Cytoscape 3! Please send your questions and comments
to our <a href="https://groups.google.com/forum/?fromgroups#!forum/cytoscape-helpdesk">
mailing list</a>.
</p>
</div>
</div>
</div>
<script src="js/footer.js"></script>
</div>
</body>
</html>