release_notes_3_2_0.html

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    <title>Cytoscape 3.2.0 Release Notes</title>

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    <meta name="author" content="Keiichiro Ono">

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        <h1 class="centering">Release Notes for Cytoscape 3.2.0</h1>
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            <img src="images/release_notes/cy32-release1.png" class="image-fit">
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                <p>
                    <a class="btn btn-primary btn-lg btn-block" href="#new_features">
                        New Features
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            <div class="col-xs-12 col-md-3">
                <p>
                    <a class="btn btn-primary btn-lg btn-block" href="#system_requirements">
                        System Requirements
                    </a>
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                    <a class="btn btn-primary btn-lg btn-block" href="#manual">
                        Manual
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                <p>
                    <a class="btn btn-warning btn-lg btn-block" href="#known_issues">
                        Known Issues
                    </a>
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<a name="new_features"></a>

<div class="white">
    <div class="container centering">
        <h1 class="centering">About Version 3.2.0</h1>

        <p class="lead light-text">
            Cytoscape 3.2.0 is the latest version of Cytoscape 3.x series with new features and bug fixes.
        </p>
    </div>
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    <div class="container image-fit">
        <img src="images/release_notes/cy32-release7.png" class="image-fit">
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    <h1 class="centering">Performance</h1>

    <div class="container">
        <div class="row item">
            <div class="col-md-6">
                <h3>Improved Network Loading Speed</h3>

                <p class="lead">
                    Network loading process is optimized and faster than 3.1.x.
                </p>
            </div>
            <div class="col-md-6">
                <h3>Improved Rendering Engine Performance</h3>

                <p class="lead">
                    Rendering engine is optimized especially for large networks. Zoom/pan is more efficient and faster
                    than past 3.x series.
                </p>
            </div>
        </div>

        <div class="row item">
            <div class="col-md-6">
                <h3>Faster Network Merge</h3>

                <p class="lead">
                    Network merge function is parallelized and is much faster for large networks.
                </p>
            </div>
            <div class="col-md-6">
                <h3>Improved Startup Speed</h3>

                <p class="lead">
                    Startup process has been optimized and startup time is shorter than 3.1.
                </p>
            </div>
        </div>
    </div>
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    <div class="container">

        <div class="row">
            <div class="col-md-5">
                <h1>Chart Editor</h1>

                <p class="lead">
                    Cytoscape 3.2 has a built-in chart editor. You can use node table data as the source of your charts
                    and render them as high-quality vector graphics. It supports standard charts including: bar, box,
                    line, pie, heatmap, and ring. In addition to charts, it supports gradients.
                </p>

                <p class="lead">
                    It is a part of Visual Style editor and you can save everything in your session file.
                </p>
            </div>
            <div class="col-md-7">
                <img src="images/release_notes/cy32-chart-editor.png">
            </div>
        </div>
    </div>
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    <div class="container image-fit">
        <h1 class="light-text">Gradient Samples:</h1>
    </div>
    <img src="images/release_notes/cy32-release5.png" class="image-fit">
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    <img src="images/release_notes/cy32-release6.png" class="image-fit">
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        <h1>Charts on Nodes:</h1>
    </div>
    <div class="container image-fit">
        <img src="images/release_notes/cy32-release-kegg1.png" class="image-fit">
        <img src="images/release_notes/cy32-release4.png" class="image-fit">
        <img src="images/release_notes/cy32-release2.png" class="image-fit">
        <img src="images/release_notes/chart-kegg.png" class="image-fit">
    </div>
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    <div class="container image-fit">
        <h1 class="centering">Interactive Web Visualization</h1>

        <p class="lead light-text">
            Cytoscape exports your session as Cytoscape.js-based web visualization. You can publish your
            networks as a complete web application. This feature is for Mac and Linux only. Support for
            Windows will be available in 3.2.1.
        </p>

        <div class="row">
            <div class="col-s-12 col-md-6">
                <h3>Original Cytoscape Session</h3>
                <img src="images/release_notes/cy32-release-web0.png" class="image-fit">
            </div>
            <div class="col-s-12 col-md-6">
                <h3>Interactive Web Visualization</h3>
                <img src="images/release_notes/cy32-release-web1.png" class="image-fit">
            </div>
        </div>
    </div>
</div>

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    <div class="container image-fit">
        <h1 class="centering">Improved Command/Tunable API</h1>

        <p class="lead light-text">
            API for Tunables and Commands are cleaned up and more stable (for developers).
        </p>
    </div>
</div>


<a name="system_requirements"></a>

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    <div class="container">
        <h1 class="centering">System Requirements</h1>

        <h3 class="warn centering">Continuing 32 bit OS Support, Deprecating Java 6 Support</h3>

        <div class="row">
            <div class="col-xs-12 col-md-offset-2 col-md-8">
                <p class="lead">
                    While v3.2 continues to support 32 bit OSs, it no longer supports Java 6. We plan to
                    support 32 bit OSs as long as we can, but will eventually drop this support.
                    Desupporting Java 6 matches current industry practice, and allows us to focus our
                    resources on more advanced feature development.
                </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 and 8). 64 bit version is recommended.
                    </li>
                    <li>Latest version of <a href="http://java.com/en/download/manual_java7.jsp">
                        Java 7 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://java.com/en/download/manual_java7.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 (Lion) and later</li>
                    <li>Latest version of <a href="http://java.com/en/download/manual_java7.jsp">Oracle Java 7</a></li>
                    <li>
                        <strong>Cytoscape no longer supports Apple Java 6.</strong>
                    </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/spreadsheet/ccc?key=0Ak5JMUI-p-wFdEJ3YV9zZ2Z4a0FNYTV5aTZEV3ZQRXc&usp=docslist_api#gid=0">these
                            distributions</a>
                    </li>
                    <li>
                        Latest version of Java 7 is required.
                    </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">About Java 8 Support</h3>

        <div class="row">
            <div class="col-xs-12 col-md-offset-2 col-md-8">
                <p class="lead">
                    Cytoscape 3.2.0 may run on Java 8, but its support is still experimental.  We recommend using Java 7 until
                    we release the official Java 8 compatible version of Cytoscape.
                </p>

            </div>
        </div>
    </div>
</div>


<a name="manual"></a>

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    <h1 class="centering">User Manual</h1>

    <div class="container">

        <div class="row">
            <div class="col-md-6 centering">
                <a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual">
                    <h3>HTML (Wiki) Version</h3>
                </a>
            </div>
            <div class="col-md-6 centering">
                <a href="manual/Cytoscape3_2_0Manual.pdf">
                    <h3>PDF version</h3>
                </a>
            </div>
        </div>
    </div>
</div>

<a name="known_issues"></a>

<div class="belt white">
    <div class="container">
        <h1 class="centering">Known Issues</h1>

        <div class="row">
            <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>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">
                <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">
                <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">
                <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>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>

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    <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 &rarr; 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>
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