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release_notes_3_0_1.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.0.1 Release Notes</title>
<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"/>
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<div id="container">
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<div id="documents">
<div class="blockfull3">
<img src="images/top_slides/cy301release.png"/>
<h2>Release Notes for Cytoscape 3.0.1</h2>
<div class="section">
<p>
Cytoscape 3.0.1 is the latest version of Cytoscape 3.x series with a lot of bug fixes.
This is the first mainstream version of Cytoscape 3 recommended for all users. There is
no major new features in this version, but we strongly recommend to upgrade if you use 3.0.0.
</p>
<h3><a href="release_notes_3_0_0.html">Learn more about new features introduced in 3.0</a></h3>
</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 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>
<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>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>
<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>
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