GSEA v3.0 Release Notes

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<h2> GSEA Desktop v3.0 Beta 3 (Apr 2017)</h2>
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<h2> GSEA Desktop v3.0 (Jul 2017)</h2>
<p>
<p>
<h3>Notes</h3>
<h3>Notes</h3>
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<ul style="margin-top:0pt;margin-bottom:0pt;">
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  <ul style="margin-top:0pt;margin-bottom:0pt;">
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<li dir="ltr" style="list-style-type:disc>GSEA Desktop v3.0 Beta 3 requires Java 8.
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    <li dir="ltr" style="list-style-type:disc>This release is open-source on [https://github.com/GSEA-MSigDB/gsea-desktop GitHub] under a [https://raw.githubusercontent.com/GSEA-MSigDB/gsea-desktop/master/LICENSE.txt BSD-style license].</li>
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<li dir="ltr" style="list-style-type:disc>Our tests show this Beta version produces equivalent results, but use the Production version if you have concerns. &nbsp;At a minimum, verification with the Production version before publication is strongly recommended.  See '[[Using GSEA v3.0 Beta Features]]' for a brief introduction and guide.
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    <li dir="ltr" style="list-style-type:disc>See [http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_GSEA_v3.0_Features Using GSEA v3.0 Features]' for a brief introduction and guide.</li>
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</ul>
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    <li dir="ltr" style="list-style-type:disc>The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v2.x).</li>
 +
    <li dir="ltr" style="list-style-type:disc>GSEA Desktop v3.0 requires Java 8.</li>
 +
  </ul>
</p>
</p>
<p>
<p>
<h3> New Features</h3>
<h3> New Features</h3>
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<ul style="margin-top:0pt;margin-bottom:0pt;">
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  <ul style="margin-top:0pt;margin-bottom:0pt;">
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     <li dir="ltr" style="list-style-type:disc>
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     <li dir="ltr" style="list-style-type:disc>Updated for the MSigDB v6.0 open-access release.</li>
-
  Updated for the MSigDB v6.0 open-access release.
+
     <li dir="ltr" style="list-style-type:disc>The Enrichment Map integration has been updated to work with current versions of Cytoscape (v3.3.0 and newer).</li>
-
     <li dir="ltr" style="list-style-type:disc>
+
    <li dir="ltr" style="list-style-type:disc>Plots and other results can now be saved in the SVG format, which provides improved resolution suitable for publication, better post-analysis editing options, etc. Use the &lsquo;Create SVG plot images&rsquo; parameter in the Advanced Fields.</li>
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  ''MSigDB XML Browser Beta 1'' has been released as a separate application. See the [http://software.broadinstitute.org/gsea/downloads.jsp Downloads page].
+
    <li dir="ltr" style="list-style-type:disc>''MSigDB XML Browser Beta 1'' has been released as a separate application to streamline the GSEA Desktop application. See the [http://software.broadinstitute.org/gsea/downloads.jsp Downloads page]. Another option for investigating genesets is the online MSigDB browser www.msigdb.org.</li>
-
</ul>
+
     <li dir="ltr" style="list-style-type:disc;>There is a new option for saving the datasets backing the report heatmaps for downstream use & visualization.  Use the &lsquo;Create GCT Files&rsquo; parameter in the Advanced Fields.  These files can be used with e.g. R, [http://www.genepattern.org GenePattern], [https://software.broadinstitute.org/morpheus/ Morpheus], or [https://software.broadinstitute.org/GENE-E/ GENE-E] among other options.</li>
-
 
+
     <li dir="ltr" style="list-style-type:disc>New improvements for long-running file transfer operations include enhanced performance through I/O buffering and compression during transfer, and the addition of a progress bar.</li>
-
 
+
    <li dir="ltr" style="list-style-type:disc>Analyses run with a ''timestamp'' random seed now record the timestamp value in the HTML Report &lsquo;Other&rsquo; section. The same seed can be reused at any time to reproduce the analysis.</li>
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<h2>GSEA Desktop v3.0 Beta 2 (Oct 2016)</h2>
+
    <li dir="ltr" style="list-style-type:disc>Implemented a feature to inform the user when a new version is available.</li>
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<h3>Notes </h3>
+
  </ul>
-
<ul style="margin-top:0pt;margin-bottom:0pt;">
+
</p>
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<li dir="ltr" style="list-style-type:disc>GSEA Desktop v3.0 Beta 2 requires Java 7 or Java 8. &nbsp;Java 8 is highly recommended.
+
<p>
-
<li dir="ltr" style="list-style-type:disc>Our tests show this Beta version produces equivalent results, but use the Production version if you have concerns. &nbsp;At a minimum, verification with the Production version before publication is strongly recommended. See '[[Using GSEA v3.0 Beta Features]]' for a brief introduction and guide.
+
-
</ul>
+
-
 
+
-
<h3>New Features</h3>
+
-
<ul style="margin-top:0pt;margin-bottom:0pt;">
+
-
     <li dir="ltr" style="list-style-type:disc;>There is a new option for saving the datasets backing the report heatmaps for downstream use & visualization.  Use the &lsquo;Create GCT Files&rsquo; parameter in the Advanced Fields.  These files can be used with e.g. R, [http://www.genepattern.org GenePattern], [https://software.broadinstitute.org/morpheus/ Morpheus], or [https://software.broadinstitute.org/GENE-E/ GENE-E] among other options.
+
-
     </li>
+
-
</ul>
+
<h3>Bug Fixes and Other Improvements</h3>
<h3>Bug Fixes and Other Improvements</h3>
<ul style="margin-top:0pt;margin-bottom:0pt;">
<ul style="margin-top:0pt;margin-bottom:0pt;">
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     <li dir="ltr" style="list-style-type:disc>Fixed an issue with running the Enrichment Map integration on Mac.
     <li dir="ltr" style="list-style-type:disc>Fixed an issue with running the Enrichment Map integration on Mac.
     </li>
     </li>
-
</ul>
 
-
 
-
<br />
 
-
<h2>GSEA Desktop v3.0 Beta 1 (Aug 2016)</h2>
 
-
 
-
<h3>Notes</h3>
 
-
<ul style="margin-top:0pt;margin-bottom:0pt;">
 
-
<li dir="ltr" style="list-style-type:disc>GSEA Desktop v3.0 Beta 1 requires Java 7 or Java 8. &nbsp;Java 8 is highly recommended.
 
-
<li dir="ltr" style="list-style-type:disc>Our tests show this Beta version produces equivalent results, but use the Production version if you have concerns. &nbsp;At a minimum, verification with the Production version before publication is strongly recommended.
 
-
</ul>
 
-
 
-
<h3 >New Features</h3>
 
-
<ul style="margin-top:0pt;margin-bottom:0pt;">
 
-
    <li dir="ltr" style="list-style-type:disc>
 
-
In an effort to streamline the GSEA desktop application, the MSigDB Browser feature has been split out into a separate application. This will see its own Beta release at some point in the future - users requiring the feature can continue to use the production GSEA Desktop v2.2.x in the interim. Another option is the online MSigDB browser www.msigdb.org.
 
-
    </li>
 
-
    <li dir="ltr" style="list-style-type:disc>Plots and other results can now be saved in the SVG format, which provides improved resolution suitable for publication, better post-analysis editing options, etc. Use the &lsquo;Create SVG plot images&rsquo; parameter in the Advanced Fields.
 
-
    </li>
 
-
    <li dir="ltr" style="list-style-type:disc>The Enrichment Map integration has been updated to work with current versions of Cytoscape (v3.3.0 and newer).
 
-
    </li>
 
-
    <li dir="ltr" style="list-style-type:disc>New improvements for long-running file transfer operations include enhanced performance through I/O buffering and compression during transfer, and the addition of a progress bar.
 
-
    </li>
 
-
    <li dir="ltr" style="list-style-type:disc>Analyses run with a ''timestamp'' random seed, now record the timestamp value in the HTML Report &lsquo;Other&rsquo; section. The same seed can be reused at any time to reproduce the analysis.
 
-
    </li>
 
-
</ul>
 
-
<h3>Bug Fixes and Other Improvements</h3>
 
-
<ul style="margin-top:0pt;margin-bottom:0pt;">
 
     <li dir="ltr" style="list-style-type:disc>Fixed an issue where &lsquo;NaN&rsquo; (division by zero) results were given a value of zero in the reports.
     <li dir="ltr" style="list-style-type:disc>Fixed an issue where &lsquo;NaN&rsquo; (division by zero) results were given a value of zero in the reports.
     </li>
     </li>
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     <li dir="ltr" style="list-style-type:disc>Cleaned up clutter in the application menus and preferences.
     <li dir="ltr" style="list-style-type:disc>Cleaned up clutter in the application menus and preferences.
     </li>
     </li>
-
     <li dir="ltr" style="list-style-type:disc>Added an override so the application can use a local GENE_SYMBOL.chip rather than FTP transfer.
+
     <li dir="ltr" style="list-style-type:disc>Better handling for the special internally-used GENE_SYMBOL and SEQ_ACCESSION CHIP files. Please do not use these as inputs to your analyses.
     </li>
     </li>
-
     <li dir="ltr" style="list-style-type:disc>In preparation for a future open-source release of the GSEA application under an OSI-approved license, we made a number of changes toward cleaning up the code base, removing / replacing a number of third-party libraries, and removing unused resources from the GSEA jar file. </li>
+
     <li dir="ltr" style="list-style-type:disc>In preparation for the open-source release, we made numerous changes toward cleaning up the code base, removing / replacing a number of third-party libraries, and removing unused resources from the GSEA jar file. </li>
</ul>
</ul>
 +
</p>

Current revision as of 02:24, 2 July 2017

GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact


Contents

GSEA Desktop v3.0 (Jul 2017)

Notes

  • This release is open-source on GitHub under a BSD-style license.
  • See Using GSEA v3.0 Features' for a brief introduction and guide.
  • The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v2.x).
  • GSEA Desktop v3.0 requires Java 8.

New Features

  • Updated for the MSigDB v6.0 open-access release.
  • The Enrichment Map integration has been updated to work with current versions of Cytoscape (v3.3.0 and newer).
  • Plots and other results can now be saved in the SVG format, which provides improved resolution suitable for publication, better post-analysis editing options, etc. Use the ‘Create SVG plot images’ parameter in the Advanced Fields.
  • MSigDB XML Browser Beta 1 has been released as a separate application to streamline the GSEA Desktop application. See the Downloads page. Another option for investigating genesets is the online MSigDB browser www.msigdb.org.
  • There is a new option for saving the datasets backing the report heatmaps for downstream use & visualization. Use the ‘Create GCT Files’ parameter in the Advanced Fields. These files can be used with e.g. R, GenePattern, Morpheus, or GENE-E among other options.
  • New improvements for long-running file transfer operations include enhanced performance through I/O buffering and compression during transfer, and the addition of a progress bar.
  • Analyses run with a timestamp random seed now record the timestamp value in the HTML Report ‘Other’ section. The same seed can be reused at any time to reproduce the analysis.
  • Implemented a feature to inform the user when a new version is available.

Bug Fixes and Other Improvements

  • Selection of multiple CHIP files for analysis is no longer allowed. This is a simplification that will permit further back-end improvements in the future.
  • Collapse Dataset is no longer allowed with a GSEA Preranked analysis. This was a rarely-used feature that caused a lot of confusion.
  • Fixed an HTML report launcher bug for users with non-English locale settings.
  • Fixed an issue with running the Enrichment Map integration on Mac.
  • Fixed an issue where ‘NaN’ (division by zero) results were given a value of zero in the reports.
  • Fixed issues handling C3 MIR Gene Sets and other gene sets with names containing comma characters.  Set the ‘Alternate Delimiter’ parameter and use a semicolon to separate gene set names.
  • Improved control layout on the lower Tool Command panel.
  • Improved layout of the result chooser panels on the Leading Edge Analysis and Enrichment Map Visualization screens.
  • Updated the Browser Launcher component to fix issues with launching the web browser.
  • Improved the error reporting when there are too few samples in the dataset.
  • Fixed some basic aspects of integration with the Mac OS X menu bar.
  • Removed Thread Controls from the UI as these rarely-used functions led to instability in the application.
  • Improved memory resource use and clean-up during GSEA report generation.
  • Fixed a failure in the Chip Chooser component when not connected to a network.
  • Cleaned up clutter in the application menus and preferences.
  • Better handling for the special internally-used GENE_SYMBOL and SEQ_ACCESSION CHIP files. Please do not use these as inputs to your analyses.
  • In preparation for the open-source release, we made numerous changes toward cleaning up the code base, removing / replacing a number of third-party libraries, and removing unused resources from the GSEA jar file.

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