Difference between revisions of "Software v2 release notes"

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<p>Software updates: v2 of the GSEA java desktop application has been released.</p>
 
<p>Software updates: v2 of the GSEA java desktop application has been released.</p>
 
<h4 class="underline">What's new in GSEA Java v2.0</h4>
 
<h4 class="underline">What's new in GSEA Java v2.0</h4>
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<p>Thanks to feedback from several users over the past year we have made changes to improve        the usability of the software. In addition, we have added a gene sets browser to view, query, map and download        gene sets from our MSigDB database.        The algorithm has <strong>not</strong> changed.        The main new features and enhancements in GSEA java v2.0 include:</p>
+
<p>Thanks to feedback from several users over the past year we have made changes to improve        the usability of the software. We have also added a few new features.        The algorithm has <strong>not</strong> changed.        The main new features and enhancements in GSEA java v2.0 include:</p>
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<ul class="starlist">
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<br /><br /><span style="font-weight: bold;">1. Leading Edge Analysis</span><br /><br />Implementation of this <br /><br /><br /><span style="font-weight: bold;">2. Documentation</span><br /><br /><br /><br /><span style="font-weight: bold;">3. Integrated Gene Sets Browser</span><br />
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    <li><strong>The industry's best i18n support:</strong> IntelliJ IDEA's greatly enhanced            internationalization support now surpasses            any other Java localization tool currently available. We even used the new functionality ourselves to create            a new version of IntelliJ IDEA            in Japanese (concurrently released by our reseller in Japan). <span class="comment"><a href="../../../features/i18n_support.html">Read more &raquo;</a></span></li>
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<p><br /></p>
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    <li><strong>Improved JavaScript and Web Development support</strong>: important improvements to JavaScript            support equip both experienced developers            and &quot;newbies&quot; with a full arsenal of features. Even AJAX development becomes quick and simple            (especially when developing AJAX libraries). <span class="comment"><a href="../../../features/javascript.html">Read            more &raquo;</a></span></li>
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<p>4. Many more gene sets along with annotations in the form of Gene Set Cards<br /></p>
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    <li><strong>New JSP debugging support</strong>: including source-level JSP debugging when remotely connected to            IBM WebSphere&trade; 5.1 or later.            <span class="comment"><a href="javascript://" onclick="openBrWindow('documentation/howto_02.html','winFullScr','scrollbars=yes,menubar=no,resizable=yes,location=yes,width=640, height=660');return BOPlaceMark();">Read                more &raquo;</a></span></li>
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<p style="font-weight: bold;"><br /></p>
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     <li><strong>More support for plug-in developers</strong>: New actions for auto-creating new application, module,            and project components; new inspections            validate the consistency of plug-in descriptors. <span class="comment"><a href="../../../features/open_api.html">Read            more &raquo;</a></span></li>
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<p style="font-weight: bold;">5. Chip2Chip</p>
 +
<br /><br />
 +
<p><span style="font-weight: bold;">6. Usability enhancements to the Java </span><span style="font-weight: bold;">Graphical User Interface</span></p>
 +
<ul>
 +
    <li>A seperate tool is provided which can run GSEA on preranked gene lists</li>
 +
     <li>Heat maps can be generated in headless mode</li>
 +
    <li>Improved performance with very large gene set databases</li>
 +
    <li>A memory monitor displays how much memory is being used / available. Clicking the icon by its side runs the garbage collector in an attempt to free up memory.</li>
 +
    <li>Added to phenotype chooser parameter is the ability to use the expression profile of a gene in the dataset as a phenotype (continuous vector) for gsea (refer to the Pegtel paper).</li>
 +
    <li>Context sensitive help- these are special help buttons distributed throughtout the java GUI. On user click they open up a URL at the GSEA doc website.</li>
 +
    <li>Default output folder can be anywhere now. Use the preferences to change the path.</li>
 +
    <li>New edb folder made with GSEA results that are a machine parsable version of enrichment results</li>
 +
    <li>Application messages can be viewed in the status bar at the bottom of the interface.</li>
 
</ul>
 
</ul>
−
<br /><br />#### List for Heidi ####<br /><br />Application messages can be viewed in the status bar at the bottom of the interface.<br />A memory monitor displays how much memory is being used / available. Clicking the icon by its side runs the garbage collector<br />in an attempt to free up memory.<br />Added to phenotype chooser parameter is the ability to use the expression profile of a gene in the dataset as a<br />phenotype (continuous vector) for gsea (refer to the Pegtel paper).<br />Splash screen displayed at application loadup<br />make sure preference options are documented<br /><br />Context sensitive help:<br />These are special help buttons distributed throughtout the java GUI. On user click they open up a URL at the GSEA doc webs ite.<br />The mappings between help button names (keys) and the URL (values) are in the file: resources/HelpURLs.txt<br />Lis these out to see which iones need special care.<br /><br />Default output folder can be anywhere now. Use the preferences to change the path.<br />&nbsp;- doc the edb as a machine parsable version of enrichment results<br /><br /><br />Main New Features<br /><br />lev<br />context sensitive help<br />headless heat map<br />better fperf with large gene set databases<br />improved pictures on reports<br />auto collapse<br />smart formats
 

Latest revision as of 19:32, 28 March 2006


Software updates: v2 of the GSEA java desktop application has been released.

What's new in GSEA Java v2.0

Thanks to feedback from several users over the past year we have made changes to improve the usability of the software. We have also added a few new features. The algorithm has not changed. The main new features and enhancements in GSEA java v2.0 include:



1. Leading Edge Analysis

Implementation of this


2. Documentation



3. Integrated Gene Sets Browser


4. Many more gene sets along with annotations in the form of Gene Set Cards


5. Chip2Chip



6. Usability enhancements to the Java Graphical User Interface

  • A seperate tool is provided which can run GSEA on preranked gene lists
  • Heat maps can be generated in headless mode
  • Improved performance with very large gene set databases
  • A memory monitor displays how much memory is being used / available. Clicking the icon by its side runs the garbage collector in an attempt to free up memory.
  • Added to phenotype chooser parameter is the ability to use the expression profile of a gene in the dataset as a phenotype (continuous vector) for gsea (refer to the Pegtel paper).
  • Context sensitive help- these are special help buttons distributed throughtout the java GUI. On user click they open up a URL at the GSEA doc website.
  • Default output folder can be anywhere now. Use the preferences to change the path.
  • New edb folder made with GSEA results that are a machine parsable version of enrichment results
  • Application messages can be viewed in the status bar at the bottom of the interface.
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