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This page provides the source code for the GSEA algorithm and desktop application. It also provides brief usage instructions, which are supplemented by the JavaDoc.

The source code is a 100% Pure Java implementation of the GSEA Algorithm from Subramanian, Tamayo, et al., 2005. The source code, instructions, and JavaDoc are intended for software engineers who want to

  • programmatically access the GSEA Java library via its API or
  • integrate the GSEA java program into their  analysis toolkit.

    Please note the license terms.

    If you are not interested in the source code and simply want to use the GSEA software, go to the Downloads.




    Contents

    Download

  • Register and download the gsea2_distrib-xx.zip file from Downloads.
  • Unzip gsea2_distrib-xx .zip using the option to create subdirectories

    This creates the following files and subdirectories:

      GSEA2-xx/
        README.txt
        LICENSE.txt
        README_BUILDING.txt
        build.xml        (an ant script that will build the source)
      src/         (GSEA java source code)
        edu/
        org/
        ...
        xtools/
      lib/        (3rd party libraries referenced by GSEA code)
        acme.jar
        algorithms.jar
        ...
        trove1.1b5.jar

    Files in the GSEA Distribution

    The GSEA distribution contains all files neccessary to build Java GSEA from source, as well as the 3rd party jar files containing GSEA's external libraries. Please check the licenses of the 3rd party jar files to make sure you are in compliance.


    Building GSEA

    • Java GSEA runs within the Java 1.6 runtime environment and should be built with a JDK version that can target that runtime environment
    • Building outside of an IDE is trivial. Once the downloaded zip file is expanded, go to the root directory (GSEA2-xx) and issue the ant command: "ant build-gsea". The ant command will compile the java sources and create a gsea2-xx.jar archive from which the GSEA desktop application and APIs may be called. The jar file should be found in the GSEA2-xx/build subdirectory.
    • If building within an IDE, you will need to reference the external libraries in the distribution's lib subdirectory.

    Note: The gsea2.jar file you might have downloaded from the website is not the same as gsea2_lib.jar. It is an optimized version of gsea2_lib.jar that has been packaged to minimize download at application startup time. Finally, the the jar file built from the java source distribution does not contain the FTP credentials required to retrieve GMT files from MSigDB. It will be necessary to contact the GSEA team at the Broad Institute to obtain these credentials.

    Tomcat / Using GSEA within a Java Server Environment: If you are working in a java server environment (for instance, Tomcat) you may notice jar conflicts which you will need to resolve.

    Important: GSEA uses the JIDE software library for its GUI. You cannot use the JIDE software library without a JIDE license.

    Feedback and Questions

    If you have issues or questions with the API usage, contact gsea@broadinstitute.org. Please include in your email the source code of your program that is causing the error.
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