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- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:3pt;"><span style="font-size:34.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">GSEA Desktop v3.0 Beta 2 Release Notes</span></p> | + | <h2> GSEA Desktop v3.0 (Jul 2017)</h2> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:18.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Released October </span><span style="font-size: 18.6667px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: 400; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">14</span><span style="font-size:18.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">, 2016</span></p> | + | <p> |
- | <br /> | + | <h3>Notes</h3> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">GSEA Desktop v3.0 Beta 2 requires Java 7 or Java 8. Java 8 is highly recommended.</span></p> | + | <ul style="margin-top:0pt;margin-bottom:0pt;"> |
- | <br /> | + | <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> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Our tests show this Beta version produces equivalent results, but use the Production version if you have concerns. At a minimum, verification with the Production version before publication is strongly recommended.</span><br />
| + | <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> |
| + | <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> |
- | <strong style="font-weight:normal;" id="docs-internal-guid-dd4158f5-8cb7-f7bf-f649-9c5aca179c33"> | + | <p> |
- | <h1 dir="ltr" style="line-height:1.38;margin-top:20pt;margin-bottom:6pt;"><span style="font-size:26.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">New Features</span></h1> | + | <h3> New Features</h3> |
- | <ul style="margin-top:0pt;margin-bottom:0pt;"> | + | <ul style="margin-top:0pt;margin-bottom:0pt;"> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Updated for the MSigDB v6.0 open-access release.</li> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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, [http://www.genepattern.org GenePattern], [https://software.broadinstitute.org/morpheus/ Morpheus], or [https://software.broadinstitute.org/GENE-E/ GENE-E] among other options. | + | <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> |
- | </span></p>
| + | <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 ‘Create SVG plot images’ parameter in the Advanced Fields.</li> |
- | </li>
| + | <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 ‘Create GCT Files’ 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> |
- | <h1 dir="ltr" style="line-height:1.38;margin-top:20pt;margin-bottom:6pt;"><span style="font-size:26.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Bug Fixes and Other Improvements</span></h1>
| + | <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> |
- | <ul style="margin-top:0pt;margin-bottom:0pt;">
| + | <li dir="ltr" style="list-style-type:disc>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.</li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Implemented a feature to inform the user when a new version is available.</li> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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.</span></p>
| + | </ul> |
- | </li>
| + | |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Collapse Dataset is no longer allowed with a GSEA Preranked analysis. This was a rarely-used feature that caused a lot of confusion.</span></p>
| + | |
- | </li>
| + | |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;">
| + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Fixed an HTML report launcher bug for users with non-English locale settings.</span></p>
| + | |
- | </li>
| + | |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Fixed an issue with running the Enrichment Map integration on Mac.</span></p>
| + | |
- | </li>
| + | |
- | </ul> | + | |
- | </strong><br class="Apple-interchange-newline" />
| + | |
- | | + | |
- | <hr />
| + | |
- | | + | |
- | <br />
| + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:3pt;"><span style="font-size:34.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">GSEA Desktop v3.0 Beta 1 Release Notes</span></p>
| + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:18.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Released August </span><span style="font-size: 18.6667px; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: 400; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">15</span><span style="font-size:18.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">, 2016</span></p>
| + | |
- | <br />
| + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">GSEA Desktop v3.0 Beta 1 requires Java 7 or Java 8. Java 8 is highly recommended.</span></p>
| + | |
- | <br />
| + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Our tests show this Beta version produces equivalent results, but use the Production version if you have concerns. At a minimum, verification with the Production version before publication is strongly recommended.</span><br />
| + | |
| </p> | | </p> |
- | <strong style="font-weight:normal;" id="docs-internal-guid-dd4158f5-8cb7-f7bf-f649-9c5aca179c33"> | + | <p> |
- | <h1 dir="ltr" style="line-height:1.38;margin-top:20pt;margin-bottom:6pt;"><span style="font-size:26.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">New Features</span></h1> | + | <h3>Bug Fixes and Other Improvements</h3> |
| <ul style="margin-top:0pt;margin-bottom:0pt;"> | | <ul style="margin-top:0pt;margin-bottom:0pt;"> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>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. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Collapse Dataset is no longer allowed with a GSEA Preranked analysis. This was a rarely-used feature that caused a lot of confusion. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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. </span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Fixed an HTML report launcher bug for users with non-English locale settings. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">The Enrichment Map integration has been updated to work with current versions of Cytoscape (v3.3.0 and newer).</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Fixed an issue with running the Enrichment Map integration on Mac. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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. </span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Fixed an issue where ‘NaN’ (division by zero) results were given a value of zero in the reports. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Analyses run with a</span><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:italic;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"> ‘timestamp’</span><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;"> 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.</span></p>
| + | |
| </li> | | </li> |
- | </ul>
| + | <li dir="ltr" style="list-style-type:disc>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. |
- | <h1 dir="ltr" style="line-height:1.38;margin-top:20pt;margin-bottom:6pt;"><span style="font-size:26.666666666666664px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Bug Fixes and Other Improvements</span></h1>
| + | |
- | <ul style="margin-top:0pt;margin-bottom:0pt;">
| + | |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Fixed an issue where ‘NaN’ (division by zero) results were given a value of zero in the reports.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Improved control layout on the lower Tool Command panel. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Improved layout of the result chooser panels on the Leading Edge Analysis and Enrichment Map Visualization screens. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Improved control layout on the lower Tool Command panel.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Updated the Browser Launcher component to fix issues with launching the web browser. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Improved layout of the result chooser panels on the Leading Edge Analysis and Enrichment Map Visualization screens.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Improved the error reporting when there are too few samples in the dataset. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Updated the Browser Launcher component to fix issues with launching the web browser.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Fixed some basic aspects of integration with the Mac OS X menu bar. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Improved the error reporting when there are too few samples in the dataset.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Removed Thread Controls from the UI as these rarely-used functions led to instability in the application. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Fixed some basic aspects of integration with the Mac OS X menu bar.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Improved memory resource use and clean-up during GSEA report generation. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Removed Thread Controls from the UI as these rarely-used functions led to instability in the application.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Fixed a failure in the Chip Chooser component when not connected to a network. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Improved memory resource use and clean-up during GSEA report generation.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <li dir="ltr" style="list-style-type:disc>Cleaned up clutter in the application menus and preferences. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Fixed a failure in the Chip Chooser component when not connected to a network.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <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. |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Cleaned up clutter in the application menus and preferences.</span></p>
| + | |
| </li> | | </li> |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"> | + | <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> |
- | <p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">Added an override so the application can use a local GENE_SYMBOL.chip rather than FTP transfer.</span></p>
| + | |
- | </li>
| + | |
- | <li dir="ltr" style="list-style-type:disc;font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;"><span style="font-size:14.666666666666666px;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap;">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. </span></li>
| + | |
| </ul> | | </ul> |
- | </strong><br class="Apple-interchange-newline" /> | + | </p> |