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release_notes_3_0_0.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.0.0 Release Notes</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="Release Notes for 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/1.9.0/jquery.min.js"></script>
<script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.10.0/jquery-ui.min.js"></script>
<script src="js/global_variables.js"></script>
<script src="js/menu_generator.js"></script>
</head>
<body>
<div id="container">
<script src="js/header.js"></script>
<div id="documents">
<div class="blockfull3">
<img src="images/cytoscape3_release_beta1.png"/>
<h2>New Features in Cytoscape 3</h2>
<div class="feature">
<img src="images/welcome_screen.png"/>
<h3>Updated Welcome Screen</h3>
<div class="text">
For convenience, Cytoscape shows <strong><i>Welcome Screen</i></strong> at
startup timewhich provides easy way to access sample data sets and public databases.
</div>
</div>
<div class="feature">
<img src="images/edge_bend_editor.png"/>
<h3>Edge Bend Visual Property</h3>
<div class="text">
Edge Bend is now a standard Visual Property.
You can use it as a part of your Visual Style.
</div>
</div>
<div class="feature">
<img src="images/edge_bundling.png"/>
<h3>Edge Bundling</h3>
<div class="text">
You can bundle edges by automatic Edge Bundling.
This feature is useful for dense network views.
</div>
</div>
<div class="feature">
<img src="images/network_annotation.png"/>
<h3>Network Annotations</h3>
<div class="text">
You can add notes and simple shapes to background or foreground of network view.
</div>
</div>
<div class="feature">
<h3>Advanced Search Function</h3>
<img src="images/advanced_search.png"/>
<div class="text">
From this version, EnhancedSearch plugin is part of core.
You can search networks using Lucene syntax.
</div>
</div>
<div class="feature">
<img src="images/table_browser.png"/>
<h3>Show All feature in Data Table Browser</h3>
<div class="text">
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.
</div>
</div>
<div class="feature">
<img src="images/network_collection.png"/>
<h3>Network Collection</h3>
<div class="text">
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.
</div>
</div>
<h2>User Manual</h2>
<div class="section">
<p>
<a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual">
HTML (Wiki) version of Cytoscape 3 Manual
</a>
</p>
<p>
<a href="manual/Cytoscape3_0_1Manual.pdf">
PDF version
</a>
</p>
</div>
<h2>System Requirments</h2>
<div class="section">
<p>
Cytoscape 3 supports the following systems:
<h3>Windows</h3>
<ul>
<li>Windows XP and newer. 64 Bit version is recommended due to memory size problem</li>
<li>64 bit version of Windows 7 or newer is recommended</li>
<li>Latest version of Java 6 or 7 from Oracle. OpenJDK and other implementations are not tested</li>
</ul>
<h3>Mac</h3>
<ul>
<li>Mac OS X 10.5 and later</li>
<li>Latest version of Apple Java 6 or Java 7 from Oracle</li>
<li><strong>Latest version of Java is required. Please install all system/Java updates before
installing Cytoscape 3. Cytoscape does not start on older versions of Apple Java 6</strong></li>
</ul>
<h3>Linux</h3>
<ul>
<li>Tested on Ubuntu 11.x and 12.x, but may work on other distributions</li>
<li>Latest version of JDK 6 or 7 from Oracle is recommended. Not tested on OpenJDK.</li>
<li>64 bit version distributions with latest version of Oracle JDK is recommended</li>
</ul>
</p>
</div>
<a name="issues"></a>
<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>Windows XP Problems</h3>
<p>
For Windows XP systems running on PCs having more than 1GB RAM,
attempting to start Cytoscape may fail (as shown in the picture below).
</p>
<img src="images/cy3_win_xp_memory_problem.png" alt="Windows XP Warning"/>
<p>
To solve the problem, execute the <strong>gen_vmoptions.bat</strong>
file to calibrate the memory allocation configured in the
Cytoscape.vmoptions file so it does not exceed 800MB.
</p>
<h3>Installation Problem on Mac OS X Lion and Mountain Lion</h3>
<p>
From Mac OS X 10.7.5, default security option is set to
allow applications only from Apple's App Store. If you try to install
Cytoscape 3 with the default setting, you will see the following warning
message:
</p>
<img src="images/cy3_mac_security_warning.png" alt="Mac Security Warning"/>
<p>
To avoid this problem, you need to change your system's security setting.
From System Preferences, you need to change <i>Allow applications
downloaded from</i> option to <strong>Anywhere</strong>.
</p>
<img src="images/cy3_mac_change_security.png" alt="Mac change security"/>
</div>
<h2>How to Report Bugs</h2>
<div class="section">
<p>
Your bug reports are very important
to improve quality of future versions 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>
<h3><a href="cy3.html">Back to Cytoscape 3 top page...</a></h3>
</div>
</div>
<script src="js/footer.js"></script>
</div>
</body>
</html>