Software Acknowledgements

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             <td><a href="http://www.intellij.com/idea/">Intellij IDEA</a><br>
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             <td><a href="http://www.intellij.com/idea/">Intellij IDEA</a></td>
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                    [[image:idea.png]]</td>
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             <td>An awesome integrated development environment for Java</td>
             <td>An awesome integrated development environment for Java</td>
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            <td>[[image:idea.png]]</td>
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             <td><a href="http://www.jgoodies.com/ www.jgoodies.com">JGoodies</a></td>
             <td><a href="http://www.jgoodies.com/ www.jgoodies.com">JGoodies</a></td>
             <td>Forms layout and java look and feel</td>
             <td>Forms layout and java look and feel</td>
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            <td></td>
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             <td><a href="http://foxtrot.sourceforge.net/docs/introduction.php">foxtrot</a></td>
             <td><a href="http://foxtrot.sourceforge.net/docs/introduction.php">foxtrot</a></td>
             <td>Java event handling mechanism for GUI's.</td>
             <td>Java event handling mechanism for GUI's.</td>
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            <td></td>
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             <td><a href="http://www.dom4j.org/">dom4j</a></td>
             <td><a href="http://www.dom4j.org/">dom4j</a></td>
             <td>XML Parser</td>
             <td>XML Parser</td>
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            <td></td>
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             <td width="28%" style="padding: 0.75pt; width: 28%; height: 64.5pt;">
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             <td><a href="http://www.lowagie.com/iText/">itext</a></td>
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            <p><font size="3">itext </font></p>
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             <td>Java PDF library</td>
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            <p><font size="3">[[image:itext.gif]]</font></p>
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             <td>[[image:itext.gif]]</td>
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            </td>
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             <td width="34%" style="padding: 0.75pt; width: 34%; height: 64.5pt;">
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            <p><font size="3">Java PDF library</font></p>
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            </td>
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             <td width="40%" style="padding: 0.75pt; width: 40%; height: 64.5pt;">
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            <p><font size="3">[http://www.lowagie.com/iText/ </font><font size="3">www.lowagie.com/iText</font><font size="3">]</font></p>
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            </td>
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             <td width="28%" style="padding: 0.75pt; width: 28%; height: 96.75pt;">
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             <td><a href="http://jakarta.apache.org/poi/hssf/index.html">Jakarta POI (especially HSSF)</a></td>
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            <p><font size="3">Jakarta POI</font></p>
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             <td>Java excel reporting</td>
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            <p><font size="3"> (especially HSSF)</font></p>
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             <td>[[image: poi-logo.png]]</td>
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            <p><font size="3">[[image: poi-logo.png]]</font></p>
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            </td>
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             <td width="34%" style="padding: 0.75pt; width: 34%; height: 96.75pt;">
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            <p><font size="3">Java excel reporting</font></p>
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            </td>
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             <td width="40%" style="padding: 0.75pt; width: 40%; height: 96.75pt;">
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            <p><font size="3">[http://jakarta.apache.org/poi/hssf/index.html </font><font size="3">jakarta.apache.org/poi</font><font size="3">]&nbsp;</font></p>
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            </td>
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             <td width="28%" style="padding: 0.75pt; width: 28%; height: 123pt;">
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             <td><a href="http://www.object-refinery.com/jfreechart/">JFreeChart</a></td>
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            <p><font size="3">JFreeChart </font></p>
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             <td>Graphing library for Java</td>
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            <p><font size="3">[[image: jfreechart.png]]</font></p>
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             <td>[[image: jfreechart.png]]</td>
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            </td>
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             <td width="34%" style="padding: 0.75pt; width: 34%; height: 123pt;">
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            <p><font size="3">Graphing library for Java</font></p>
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            </td>
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             <td width="40%" style="padding: 0.75pt; width: 40%; height: 123pt;">
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            <p><font size="3">[http://www.object-refinery.com/jfreechart/ </font><font size="3">www.object-refinery.com/jfreechart</font><font size="3">]&nbsp;</font></p>
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             <td width="28%" style="padding: 0.75pt; width: 28%; height: 82.5pt;">
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             <td><a href="http://www.junit.org/index.htm">JUnit</a></td>
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            <p><font size="3">JUnit </font></p>
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             <td>Unit testing API</td>
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            <p><font size="3">[[image: junit.gif]]</font></p>
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             <td>[[image: junit.gif]]</td>
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             <td width="34%" style="padding: 0.75pt; width: 34%; height: 82.5pt;">
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            <p><font size="3">Unit testing API</font></p>
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            </td>
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             <td width="40%" style="padding: 0.75pt; width: 40%; height: 82.5pt;">
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            <p><font size="3">[http://www.junit.org/index.htm </font><font size="3">www.junit.org</font><font size="3">]&nbsp;</font></p>
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         <tr style="height: 130.5pt;">
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Revision as of 19:24, 16 October 2012

<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> | <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>

GSEA implementations use many software tools and libraries, several of which are open source or freely available. Our thanks to their developers.

<tbody> </tbody>
<a href="http://www.jidesoft.com jidesoft.com">Jide Software</a> Java/Swing components
<a href="http://www.oracle.com/technetwork/java/index.html http://www.oracle.com/technetwork/java/index.html">The Java 2 Platform Language that the GSEA desktop application is written in image:duke.gif
<a href="http://www.r-project.org/index.html www.r-project.org">The R programming language</a> Language that the GSEAP-P-R is written in image:Rlogo.jpg
<a href="http://www.intellij.com/idea/">Intellij IDEA</a> An awesome integrated development environment for Java image:idea.png
<a href="http://www.jgoodies.com/ www.jgoodies.com">JGoodies</a> Forms layout and java look and feel
<a href="http://foxtrot.sourceforge.net/docs/introduction.php">foxtrot</a> Java event handling mechanism for GUI's.
<a href="http://www.dom4j.org/">dom4j</a> XML Parser
<a href="http://www.lowagie.com/iText/">itext</a> Java PDF library image:itext.gif
<a href="http://jakarta.apache.org/poi/hssf/index.html">Jakarta POI (especially HSSF)</a> Java excel reporting image: poi-logo.png
<a href="http://www.object-refinery.com/jfreechart/">JFreeChart</a> Graphing library for Java image: jfreechart.png
<a href="http://www.junit.org/index.htm">JUnit</a> Unit testing API image: junit.gif

log4j

image:log4j.jpg

Logging toolkit for Java

jakarta.apache.org/log4j 

Oro

Regular expressions library in Java

jakarta.apache.org/oro 

Trove

High performance collections library from GNU

trove4j.sourceforge.net 

ECS

Element construction set (a HTML tag library from Apache  <st1:place w:st="on"><st1:city w:st="on">Jakarta</st1:city></st1:place>)

jakarta.apache.org

Xenu link sleuth

Website broken link checker

home.snafu.de/tilman/xenulink

Personal tools