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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.1.1 Release Notes</title>
<meta name="description" content="Release Notes for Cytoscape 3.1.1">
<meta name="author" content="Keiichiro Ono">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
<link rel="stylesheet" href="https://netdna.bootstrapcdn.com/bootstrap/3.1.0/css/bootstrap.min.css">
<script src="https://netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js"></script>
<link href="css/main.bootstrap.css" rel="stylesheet">
<script src="js/cytoscape.js-2.1.0/cytoscape.min.js"></script>
</head>
<body>
<div class="light-gray">
<div class="white image-wide">
<img src="images/3_1_title3.png" />
</div>
<div class="container">
<h2>Release Notes for Cytoscape 3.1.1</h2>
</div>
</div>
<div class="narrow light-gray">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#bug_fixes">
Bug Fixes
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#system_requirements">
System Requirements
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-primary btn-lg btn-block" href="#manual">
Manual
</a>
</p>
</div>
<div class="col-xs-12 col-md-3">
<p>
<a class="btn btn-warning btn-lg btn-block" href="#known_issues">
Known Issues
</a>
</p>
</div>
</div>
</div>
</div>
<a name="bug_fixes"></a>
<div class="snow-white">
<div class="container">
<h2>About Version 3.1.1</h2>
<p class="lead">
Cytoscape 3.1.1 is a bug-fix release of Cytoscape 3.x series. This is a mainstream release of Cytoscape 3 and is recommended for all users.
</p>
</div>
</div>
<div class="belt white">
<div class="container">
<h3>Major Bug Fixes</h3>
<p class="lead">
The following major issues have been fixed in Cytoscape 3.1.1.
<ul>
<li><a href="http://code.cytoscape.org/redmine/issues/2465">#2465: DialogTaskManager/CyTableImpl threw: column already exists ... 'layoutAlgorithm'</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2055">#2055: JVM SIGSEGV appears on Cytoscape startup/shutdown on Ubuntu 13.04+Oracle Java 7</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2511">#2511: Mappings sometimes not applied when restoring session</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2514">#2514: Session saved with equation return type not matching column type results in instability when reloaded</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2516">#2516: Filters not cleared when starting/loading new session</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2548">#2548: ConcurrentModificationException When Recreating CyNetworkViews</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2653">#2653: Command processing using "-S" is broken</a></li>
<li><a href="http://code.cytoscape.org/redmine/issues/2586">#2586: Ding deadlock in 3.1.1</a></li>
</ul>
</p>
<p>
For complete list of fixed bugs, please visit our <a href="http://code.cytoscape.org/redmine/projects/cytoscape3/issues?utf8=%E2%9C%93&set_filter=1&f%5B%5D=fixed_version_id&op%5Bfixed_version_id%5D=%3D&v%5Bfixed_version_id%5D%5B%5D=15&f%5B%5D=&c%5B%5D=tracker&c%5B%5D=status&c%5B%5D=priority&c%5B%5D=subject&c%5B%5D=assigned_to&c%5B%5D=updated_on&group_by=">
issue tracker web site.</a> More details are available in the last section of <a href="cy3_welcome_letter_v11.pdf">Welcome Letter</a>.
</p>
</div>
</div>
<a name="system_requirements"></a>
<div class="belt snow-white">
<div class="container">
<h2>System Requirements</h2>
<h4 style="color: red">Important: Cytoscape 3.1.1 is not compatible with Java 8. Please use Java 6 or 7 instead.</h4>
<p class="lead">
Cytoscape 3.1.1 supports the following systems:
</p>
<div class="row">
<div class="col-xs-12 col-md-4">
<h3>Windows</h3>
<ul>
<li>Windows XP and newer (including Windows 7 and 8). 64 bit version is recommended for larger networks.
</li>
<li>Latest version of Java 6 or 7 from Oracle. OpenJDK and other implementations are not tested.
</li>
<li>Note that the java.com website installs a 32 bit JVM by default (to match Windows’ 32 bit browsers). To download a 64 bit JVM, use <a href="http://java.com/en/download/manual.jsp">this page</a>.
</li>
</ul>
</div>
<div class="col-xs-12 col-md-4">
<h3>Mac</h3>
<ul>
<li>Mac OS X 10.7 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>
</div>
<div class="col-xs-12 col-md-4">
<h3>Linux</h3>
<ul>
<li>Tested on CentOS 6, Fedora 19/20, and Ubuntu 12.x/13.x/14.x, but may work on other distributions</li>
<li>
Latest version of Java 6 or 7 from Oracle, or latest version of OpenJDK 7. Earlier versions of OpenJDK are not tested.
</li>
<li>
For Ubuntu, 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>.
</li>
</ul>
</div>
</div>
</div>
</div>
<a name="manual"></a>
<div class="belt light-gray">
<div class="container">
<h2>User Manual</h2>
<div class="row">
<div class="col-md-6">
<a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual">
<h3>HTML (Wiki) Version</h3>
</a>
</div>
<div class="col-md-6">
<a href="manual/Cytoscape3_1_0Manual.pdf">
<h3>PDF version</h3>
</a>
</div>
</div>
</div>
</div>
<a name="known_issues"></a>
<div class="belt snow-white">
<div class="container">
<h2>Known Issues</h2>
<div class="row">
<div class="col-md-4 panel snow-white">
<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>
<h3>Privacy</h3>
<p>
The latest privacy policy is posted
<a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual/Privacy">here</a>.
</p>
<h3>Proxy Settings</h3>
<p>
On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.
</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>
</div>
<div class="col-md-4 panel snow-white">
<h3>Deprecating Support for 32 bit OSs and Java 6</h3>
<p>
While v3.1 has both 32 bit OS and Java 6 support, we plan to remove support for these configurations in Cytoscape v3.2, which is under development and will likely be released in the later third of 2014. This matches current industry practice, and allows
us to focus our resources on more advanced feature development. Once v3.2 is released, we will continue to make previous Cytoscape versions available, and they will continue to have 32 bit OS and Java 6 support.
</p>
<h3>Missing Edge Columns After Loading Multiple Networks</h3>
<p>
When loading multiple networks into the same network collection, it is important to import edge tables only after each of the networks is loaded. Interspersing edge table imports with network loads may cause edge columns to become inaccessible to some
networks. Node columns are unaffected by this issue.
</p>
</div>
<div class="col-md-4 panel snow-white">
<h3>Java 6 used on Mac, even with Java 7 installed</h3>
<p>
On the Mac platform, Java 6 will be used by default (and automatically installed if necessary), even if Oracle Java 7 is installed. To use Oracle Java 7, you will have to set the JAVA_HOME environment variable to the Java 7 installation path.
</p>
<p>
To do this automatically on startup, add the following line to the .bashrc file in your home directory:
</p>
<pre>
export JAVA_HOME=$(/usr/libexec/java_home)
</pre>
<p>
And the following to the .profile file in your home directory:
</p>
<pre>
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi
</pre>
<p>
Note that this only applies to Cytoscape instances launched from the command line using the cytoscape.sh script - Java 7 is not supported when launching from the GUI. This issue will be resolved in a future release.
</p>
</div>
</div>
<div class="row">
<div class="col-md-4">
<h3>File Encoding</h3>
<p>
On all platforms, all Cytoscape session files recorded since v3.0.1 are 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>
</div>
<div class="col-md-4">
<h3>Missing Organism Networks on Welcome Screen</h3>
<p>
Users upgrading from previous Cytoscape versions (e.g., 3.0.2) may notice that the Welcome Screen contains only six of the eight organism networks shown in the user manual. To add the two new networks, terminate Cytoscape, remove the biogrid directory
in the CytoscapeConfiguration directory, and restart Cytoscape. For more information on the <strong>CytoscapeConfiguration</strong> directory, see <a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual/Launching_Cytoscape">Launching
Cytoscape in manual</a>.
</p>
</div>
<div class="col-md-4">
<h3>Executing Scripts from Command Line</h3>
<p>
Executing Cytoscape command scripts using the -S (or —script) command line option may not work if an app does not start properly or no apps are installed. If you are experiencing this issue on a clean install of Cytoscape, installing a small app (such
as Cy3PerformanceReporter) should resolve the problem. Additionally, relative file paths are not supported by -S/—script, nor are any paths with backslashes, spaces, or colons. As an alternative, command scripts can be executed
using the Tools-Execute Command File menu item.
</p>
</div>
</div>
<div class="row">
<div class="col-md-4 panel snow-white">
</div>
</div>
</div>
</div>
<div class="belt light-gray">
<div class="container">
<div class="row">
<div class="col-md-6">
<h2>How to Report Bugs</h2>
<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>
<div class="col-md-6">
<h2>Need Help?</h2>
<p class="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>
</div>
<footer></footer>
<script src="js/load_cyjs.js"></script>
<script src="js/setup_page.js"></script>
</body>
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