geWorkbench

Download Instructions | License Information

Software Requirements

To run geWorkbench you will need to have Sun Java J2SE 5.0 or higher installed on your computer (this is also refered to as the Java 1.5 JRE). If the JRE is not already installed on your computer you can get it from Sun's Java Web site, http://java.sun.com/j2se/1.5.0/download.jsp. geWorkbench is downloaded as a self-installing package with support for Windows, Linux and MAC OS-X.

Hardware Requirements

Testing of geWorkbench is done on machines with 1 GB of memory and this is now a suggested minimum configuration, though the program will work for many tasks with 512 MB. Working with large datasets (100s of arrays) may require additional memory.

IMPORTANT NOTICE ABOUT LICENSE

Use of geWorkbench is governed by the rules specified in the software license. Please make sure to read the license and understand your obligations before proceeding to download the application.

Downloads

Up to date versions of geWorkbench (current version -> 1.5.0) and the geWorkbench Software Development Kit (current version -> 1.0.1) can be downloaded from the project page at NCI's GForge repository:

  http://gforge.nci.nih.gov/frs/?group_id=78

If you wish to receive announcements about new application and SDK releases please subscribe to the mailing list geworkbench-announce@gforge.nci.nih.gov. Other available mailing lists are described in the Community section of our site.

Installation Instructions

You must have the Java 1.5 JRE installed before installing geWorkbench.

1. Windows Vista/Generic

      The particular version of the installer
      program used to package geWorkbench does not work under
      Microsoft Vista.  A non-installer-based version of
      geWorkbench is supplied in a Zip file which will work on
      any platform, including Microsoft Vista.

      File: geWorkbench_v1.5.0_Vista_and_Generic.zip

      Installation: 
   
         *  Unzip the file.  It will create a directory
            geWorkbench1.5.
         

      Running geWorkbench:

         * You must have at least the Java 1.5 JRE/JDK installed.
         * Open a command/console window and change to the
           newly created geWorkbench directory.
             # Windows/Vista: type "launch_geWorkbench.bat".
             # Linux/Unix:    type "launch_geworkbench.sh".

             # Alternatively, if you have Apache Ant installed,
               you can type "ant run".

2. Windows (non-Vista)

      File: geWorkbench_v1.5.0_Windows_installer.exe

3. MacOSX

      File: geWorkbench_v1.5.0_MacOSX_installer.zip

4. Linux

      File: geWorkbench_v1.5.0_Linux_installerV1.bin - for older versions of Linux.
      File: geWorkbench_v1.5.0_Linux_installerV2.bin - for newer versions of Linux.

      (again, this is due to an incompatibility in the installer program).

Windows Instructions:

• After downloading, double-click geWorkbench_v1.5.0_Windows_installer.exe

Mac OS X Instructions:

• After downloading, double-click geworkbench_v1.5.0 Mac_installer.zip

• Notes
  • Requires Mac OS X 10.4 or later
  • The compressed installer should be recognized by Stuffit Expander and should automatically be expanded after downloading. If it is not expanded, you can expand it manually using StuffIt Expander 6.0 or later.
  • If you have any problems launching the installer once it has been expanded, make sure that the compressed installer was expanded using Stuffit Expander.

Linux Instructions:

To run the installation process or geWorkbench, you may need to set up several environment variables.

• If you downloaded the version of geWorkbench without the Java JRE, you must check that the following two variables are set (example values are given, please substitute paths specific to your own machine):

JAVA_HOME=/opt/jdk1.5.0_15

PATH=/opt/jdk1.5.0_15/bin:$PATH

Depending on the X Windows server you are running, you may also need to set your X Windows DISPLAY variable; the installer requires X windows to display installation status:

DISPLAY=(your IP):0

• After downloading, cd to the directory where you downloaded the installer.
• At the prompt type: sh ./install.bin (where install.bin is the name of the file you downloaded, it will actually be version specific).

Please see the Known Issues section if you experience problems installing or running geWorkbench under Linux.

Tutorial data

tutorial_data.zip (3.586 MB) - data files in several different formats useful for the tutorials or just trying out geWorkbench.

Bcell-100.zip (5.256 MB) - This file is the same as webmatrix2.exp below, but with the array subsets given more descriptive names.

webmatrix2.zip (5.647 MB) - a large (100 array) microarray dataset in the geWorkbench matrix format. Data is from the lab of Riccardo Dalla-Favera, Columbia University, and is provided only for use in learning and testing geWorkbench.

Training Slides

A set of PowerPoint training slides has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval. It follows the outline structure specified in the caBIG training guidelines. The PowerPoint file is available from the Project Documentation section of this site.