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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape 3.5.0 Release Notes</title>
<meta name="description" content="Release Notes for Cytoscape 3.5.0">
<meta name="author" content="Keiichiro Ono">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.4.min.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css" integrity="sha512-dTfge/zgoMYpP7QbHy4gWMEGsbsdZeCXz7irItjcC3sPUFtf0kuFbDz/ixG7ArTxmDjLXDmezHubeNikyKGVyQ==" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js" integrity="sha512-K1qjQ+NcF2TYO/eI3M6v8EiNYZfA95pQumfvcVrTHtwQVDG+aHRqLi/ETn2uB+1JqwYqVG3LIvdm9lj6imS/pQ==" crossorigin="anonymous"></script>
<link href="css/main.bootstrap.css" rel="stylesheet">
<!-- For Scroll -->
<script src="js/smooth-scroll.min.js"></script>
</head>
<body>
<div class="white belt">
<div class="container">
<h1 class="centering">Release Notes for Cytoscape 3.5.0</h1>
</div>
<div class="container">
<div class="row">
<img src="images/screenshots/cy3_5_0_desktop.png" class="image-fit">
</div>
</div>
</div>
<div class="narrow white">
<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" data-scroll>
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" data-scroll>
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" data-scroll>
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" data-scroll>
Known Issues
</a>
</p>
</div>
</div>
</div>
</div>
<div id="new_features" class="white">
<div class="container centering">
<h1 class="centering">About Version 3.5.0</h1>
<p class="lead light-text">
Cytoscape 3.5 is a Cytoscape Desktop version with updated user interface
</p>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-md-5">
<h2>ID Mapper</h2>
<p class="lead">
ID mapping is a classic problem in bioinformatics. Now you don't have to use external tools to do the mapping. You can directly call the ID mapping service from the table browser.
</p>
</div>
<div class="col-md-7">
<img src="images/release_notes/cy3_5_0_id_mapping.png">
</div>
</div>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-md-5">
<img src="images/release_notes/cy3_5_0_node_layout_tool.png">
</div>
<div class="col-md-7">
<h2>Node Layout Tools</h2>
<p class="lead">
In 3.5, all of the manual node layout tools are consolidated into one panel for tweaking layouts.
</p>
</div>
</div>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-md-5">
<h2>Improved Export Dialog</h2>
<p class="lead">
When you export network views to images, you can specify DPI directry to create proper resolution bitmap images.
</p>
</div>
<div class="col-md-7">
<img src="images/release_notes/cy3_5_0_export_dialog.png">
</div>
</div>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-md-6">
<h2>Drag & Drop Support</h2>
<p class="lead">
To load networks and data tables from files, you can simply drag & drop them onto Network Panel / Table Browser.
</p>
</div>
<div class="col-md-6">
<h2>Long Running Remote Task API</h2>
<p class="lead">
This feature is for App developers. To execute long running remote tasks, such as network analysis or layout using remote computing clusters, app developers can use this API to manage those tasks.
</p>
</div>
</div>
</div>
</div>
<div class="narrow white">
<div class="container">
<div class="row">
<div class="col-md-6">
<h2>Compound Spring Embedder (CoSE) Layout</h2>
<p class="lead">
For grouped nodes rendered as compound nodes, you can apply CoSE algorithm for better result.
</p>
</div>
<div class="col-md-6">
<h2>Faster Row Deletion</h2>
<p class="lead">
Table row deletion is much faster than the previous version.
</p>
</div>
</div>
</div>
</div>
<div id="system_requirements" class="narrow white">
<div class="container">
<h1 class="centering">System Requirements</h1>
<h3 class="warn centering">Continuing 32 bit OS Support, Deprecating Java 6 & 7 Support</h3>
<div class="row">
<div class="col-xs-12 col-md-offset-2 col-md-8">
<p class="lead">
While v3.5 continues to support 32 bit OSs, it no longer supports Java 6 or 7. We plan to support 32 bit OSs as long as we can, but will eventually drop this support. Desupporting Java 6 and 7 matches current industry practice, and allows us to focus
our resources on more advanced feature development.
</p>
</div>
</div>
<h3 class="warn centering">Not Supporting Java 9 Yet</h3>
<div class="row">
<div class="col-xs-12 col-md-offset-2 col-md-8">
<p class="lead">
We hope to support Java 9 in the next release of Cytoscape, which is now in the works. Please use Java 8, as described below.
</p>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-4">
<h3>Windows</h3>
<ul>
<li>Windows XP and newer (including Windows 7, 8 and 10). <strong>64 bit version is recommended</strong>.
</li>
<li>Latest version of <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html">
Java 8 from Oracle</a>. 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://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html">this
page</a>.
</li>
</ul>
</div>
<div class="col-xs-12 col-md-4">
<h3>Mac</h3>
<ul>
<li>Mac OS X 10.9 (Mavericks) and later</li>
<li>Latest version of <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html">Oracle Java 8</a></li>
</ul>
</div>
<div class="col-xs-12 col-md-4">
<h3>Linux</h3>
<p>
</p>
<ul>
<li>Tested on
<a href="https://docs.google.com/spreadsheets/d/1dkP-82icfrdQp3vqt8HqzeyGb_iwgrqg3OxJaqOuWiI/edit#gid=0&vpid=A1">these
distributions</a>
</li>
<li>
Latest version of Java is required (minimum Java 8 Update 72).
</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>
<h3 class="warn centering">Java 8 is Required</h3>
<div class="row">
<div class="col-xs-12 col-md-offset-2 col-md-8">
<p class="lead">
Cytoscape 3.5.0 requires Java 8. You should install latest version of Java 8.
</p>
</div>
</div>
</div>
</div>
<div id="manual" class="narrow snow-white">
<h1 class="centering">User Manual</h1>
<div class="container">
<div class="row">
<div class="col-md-6 centering">
<a href="http://manual.cytoscape.org/">
<h3>HTML Version</h3>
</a>
</div>
<div class="col-md-6 centering">
<a href="manual/Cytoscape3_5_0Manual.pdf">
<h3>PDF version</h3>
</a>
</div>
</div>
</div>
</div>
<div id="known_issues" class="belt white">
<div class="container">
<h1 class="centering">Known Issues</h1>
<div class="row">
<div class="col-md-4 panel">
<h3>Missing Scrollbars on Linux</h3>
<p>
A bug in Java 8 Update 60 (also present in 65/66) causes scrollbars to not always appear on Linux systems. This occurs on both OpenJDK and Oracle Java releases (including the OpenJDK shipped with Ubuntu 15.10 and some other recent Linux distributions),
and is resolved by installing Java 8 Update 72 or later from Oracle.
</p>
</div>
<div class="col-md-4 panel">
<div class="row">
<div class="col-md-12">
<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="row">
<div class="col-md-12">
<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>
<div class="col-md-4 panel">
<div class="row">
<div class="col-md-12">
<h3>Proxy Settings</h3>
<p>
On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.
</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<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>
</div>
<div class="row">
<div class="col-md-4 panel">
<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">
<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 panel">
<h3>Installing on Ubuntu 15.10 (64 bit)</h3>
<p>
The Cytoscape installer does not run on non-root accounts using the default OpenJDK JVM. It works properly with Oracle Java 8 Update 71 or higher, or as root with OpenJDK. Alternatively, Cytoscape can be installed by downloading and unzipping the GZIP
archive found via the <a href="download-platforms.html">Other Platforms link on the Download page</a>.
</p>
</div>
</div>
<div class="row">
<div class="col-md-4 panel">
<h3>Fedora 21+: Headless Java</h3>
<p>
Fedora 21 (or later) installs a headless (non-GUI) version of Java by default. As a GUI application, Cytoscape will not install or run with this version of Java. To use Cytoscape on Fedora 21 (or later), one will need to install a standard version of
Java. The OpenJDK JRE is available from the Fedora package repository - simply install the java-1.8.0-openjdk.x86_64 (for 64-bit) or java-1.8.0-openjdk.i686 (ofor 32-bit) packages. Oracle’s JRE is available for download in RPM
format at java.com, though this requires extra configuration.
</p>
</div>
<div class="col-md-4 panel">
<h3>Fedora 21+: Blank Startup Screen</h3>
<p>
On Fedora 21 (or later), the Cytoscape splash screen may appear blank on startup. This does not affect the operation of the Cytoscape application, and can be resolved by upgrading to Fedora 23 with latest patches.
</p>
</div>
</div>
</div>
</div>
</div>
<div class="belt light-blue">
<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>
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