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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.1.0 Release Notes</title>
<meta name="description" content="Release Notes for Cytoscape 3.1.">
<meta name="author" content="Keiichiro Ono">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.0.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/3.1.0/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 3.1.0</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="#new_features">
New Features
</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="new_features"></a>
<div class="snow-white">
<div class="container">
<h2>About Version 3.1.0</h2>
<p class="lead">
Cytoscape 3.1 is the latest version of Cytoscape 3.x series with many new features and bug fixes. This is a mainstream release of Cytoscape 3 and is recommended for all users.
</p>
</div>
</div>
<div class="belt white">
<div class="container">
<div class="row">
<div class="col-md-5">
<img src="images/screenshots/31_vizmap.png">
</div>
<div class="col-md-7">
<h3>New Style Editor</h3>
<p class="lead">
Cytoscape 3.1.0 has a new Visual Style editor. It is more intuitive, and easy to use.
</p>
</div>
</div>
<div class="row">
<div class="col-md-5">
<h3>New Filter</h3>
<p class="lead">
New Filter is much faster than the last version. User interface is also updated for handling more complex queries in real time.
</p>
</div>
<div class="col-md-7">
<img src="images/screenshots/31_filter.png">
</div>
</div>
<div class="row item">
<div class="col-md-8">
<img src="images/screenshots/31_js1.png" width="100%">
</div>
<div class="col-md-4">
<h3>Export to JSON</h3>
<p class="lead">
Cytoscape 3.1.0 can export networks, tables, and Visual Styles into cytoscape.js compatible JSON format. This means you can use network visualizations created with Cytoscape in web browsers. (Try it in the window below.)
</p>
</div>
</div>
<div class="row item">
<div class="cyjs" style="height: 500px">
</div>
</div>
<div class="row item">
<div class="col-md-6">
<img src="images/screenshots/31_command.png">
</div>
<div class="col-md-6">
<h3>Commands and Its REST API</h3>
<p>
Basic Cytoscape functions, such as Layout, or export to files, can be accessed through Cytoscape Commands. You can automate your workflow by writing simple Command files. Commands are accessible from REST API.
</p>
</div>
</div>
<div class="row item">
<div class="col-md-5">
<h3>Updated Welcome Screen</h3>
<p class="lead">
New Welcome Screen with more preset data sets.
</p>
</div>
<div class="col-md-7">
<img src="images/screenshots/31_welcome.png">
</div>
</div>
<div class="row item">
<div class="col-md-8">
<img src="images/screenshots/31_psicquic.png">
</div>
<div class="col-md-4">
<h3>Updated Remote Database Client</h3>
<p class="lead">
New remote data access client (
<a href="https://code.google.com/p/psicquic/">PSICQUIC</a> Client) is faster, and more stable. It supports new MITAB 2.7 table columns.
</p>
</div>
</div>
</div>
</div>
<a name="system_requirements"></a>
<div class="belt snow-white">
<div class="container">
<h2>System Requirements</h2>
<p class="lead">
Cytoscape 3.1 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 10.5 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>
</div>
<div class="col-xs-12 col-md-4">
<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 CentOS 6, Fedora 19/20, and Ubuntu 11.x/12.x/13.x, but may work on other distributions</li>
<li>
For JDK6, latest version from Oracle is recommended. For JDK7, latest version of OpenJDK is recommended. (Oracle JDK7 has known stability issues on Ubuntu, but may work on other distributions.)
</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>Proxy Settings</h3>
<p>
On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.
</p>
</div>
<div class="col-md-4 panel snow-white">
<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 panel snow-white">
<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>
<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>
</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>
</div>
<div class="col-md-4 panel snow-white">
<h3>Privacy</h3>
<p>
The latest privacy policy is posted
<a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual/Privacy">here</a>.
</p>
</div>
</div>
<div class="row">
<div class="col-md-4">
<h3>Missing Columns After Loading Multiple Networks</h3>
<p>
When loading multiple networks into the same network collection, it is important to import tables only after each of the networks is loaded. Interspersing table imports with network loads may cause some table columns to become inaccessible to some networks.
</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>
</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>
</html>