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release_notes_3_0_2.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.0.2 Release Notes</title>
<meta name="description" content="Release Notes for Cytoscape 3.">
<meta name="author" content="Keiichiro Ono">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="css/bootstrap.min.css" rel="stylesheet">
<link href="css/main.bootstrap.css" rel="stylesheet">
<script src="http://ajax.googleapis.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>
<script src="js/bootstrap.min.js"></script>
</head>
<body>
<header></header>
<nav></nav>
<div class="belt blue">
<div class="container text-center">
<img src="images/screenshots/cy302release.png"/>
<h2>Release Notes for Cytoscape 3.0.2</h2>
</div>
</div>
<div class="belt white">
<div class="container">
<p class="lead">
Cytoscape 3.0.2 is the latest version of Cytoscape 3.x series with many bug fixes.
This is a mainstream release of Cytoscape 3 and is recommended for all users.
</p>
<h2>User Manual</h2>
<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>
<h2>System Requirements</h2>
<p class="lead">
Cytoscape 3 supports the following systems:
</p>
<h3>Windows</h3>
<ul>
<li>Windows XP and newer. 64 Bit version is recommended for larger networks</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>
<h4>Windows 8</h4>
<p>
While Windows 8 is a 64 bit system, the Java.com web site installs a 32 bit JVM by default
under the theory that it is important for the JVM to match Windows 8’s Internet Explorer browser
(also 32 bit). For best results with Cytoscape, you should install the 64 bit JVM, available
at <a href="http://java.com/en/download/manual.jsp">this page</a>.
</p>
<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>
<p>
For Linux, a simple way of installing the Oracle JVM is described
<a href="http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html.">here</a>.
</p>
<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>
<a name="issues"></a>
<h2>Known Issues</h2>
<div id="mac-java">
<h3 style="color: red">Mac and the Java Virtual Machine</h3>
<p>
There is a known issue with a recent Java update distributed by Apple --
it causes Cytoscape not to start up properly. This can occur even if you've
installed the latest version of Oracle Java 7 as Cytoscape uses the Apple JVM.
To find out if you have the problematic update, run the following command in a Terminal window:
<h4><strong>/usr/libexec/java_home -v 1.6 -exec java -version</strong></h4>
If the output contains “xM4508”, you have the broken version. In that case,
you will need to install the latest update from Apple according to your OS version:
</p>
<p>
<ul>
<li>
<a href="http://support.apple.com/kb/DL1572">http://support.apple.com/kb/DL1572</a>
(for OS X 10.7, 10.8+)
</li>
<li>
<a href="http://support.apple.com/kb/DL1573">http://support.apple.com/kb/DL1573</a>
(for OS X 10.6)
</li>
</ul>
</p>
</div>
<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>
<h4>Ubuntu and Java 7</h4>
<p>
Ubuntu 13.04 with Java 7 has known stability issues with
Cytoscape 3.x - please use Java 6 or an earlier version of Ubuntu as a workaround.
</p>
<h3>Proxy Settings</h3>
<p>
On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.
</p>
<h3>File Encoding</h3>
<p>
On all platforms, all Cytoscape session files are now encoded in UTF-8 instead of the native
language encoding. This makes session files portable between workstations in all locales. Users in
Japan, Korea, and China are most affected – existing v3.0.0 or v2.x session files must be translated
to UTF-8 using a platform-dependent editor (which most users are already using for this purpose).
Users in Europe and the Americas are affected, too, if they use characters beyond the standard ANSI
128 – they can translate to UTF-8 using a platform-dependent editor (e.g., Notepad for Windows).
</p>
<h3>Conflict with Older Versions</h3>
<p>
On all platforms, users installing Cytoscape directly from a ZIP or TAR file should manually clear
the Cytoscape cache by deleting the CytoscapeConfiguration folder in the user’s home directory.
</p>
<h3>Internationalization (PDF Export)</h3>
<p>
For Japanese, Korean, and Chinese users, rendering a network to a PDF file can result in loss of
labeling information in the PDF. As a workaround, users can generate any type of image file and use
the image file instead.
</p>
</div>
</div>
<div class="belt orange">
<div class="container">
<div class="row">
<h2 class="col-lg-6">How to Report Bugs</h2>
<h2 class="col-lg-6">Need Help?</h2>
</div>
<div class="row">
<div class="col-lg-6">
<p class="lead">
Your bug reports are very important
to improve quality of future versions of Cytoscape 3. If you notice any problems,
please report them from:
</p>
<blockquote>Help → Report a bug...</blockquote>
<p class="lead">
Or, you can directly report it from
<a href="http://chianti.ucsd.edu/cyto_web/bugreport/bugreport.php">Report a bug</a>
link on the navigation bar.
</p>
</div>
<p class="col-lg-6 lead">
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>
<footer></footer>
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