Application Build: 246     Database Build: 2008-04

Core Application

• Verify that your machine satisfies the system requirements
• Download the GoMiner™ program file, gominer.jar
• Install the optional components (if any) listed below you want to use.
• Either double-click the jar file, or run "java -jar gominer.jar" from the command line
• For large input files (>10,000 genes) run "java -Xms256M -Xmx256M -jar gominer.jar"
  This will allocate more memory to run the application.
• For optimal performance, install a local copy of the server and database.

Install Helper Applications

The first two helper applications are web browser components, and provide additional visualization features.

SVG Viewer

You need an SVG-capable web browser. The most common options are to use Internet Explorer (IE) with the Adobe SVG Viewer plug-in or to use the Firefox web browser. If the Adobe SVG Viewer is not already installed, you can download the installer from Adobe, and then run it. Firefox has native SVG capability, and does not require the plug-in.

If you are using a different SVG viewer on your platform, there is an option in GoMiner to save SVG's to a file, so you can open it with another viewer.

NCBI Cn3D Viewer

NCBI Cn3D Viewer provides a tool to view 3D molecular structures from the NCBI ENTREZ STRUCTURE database

• On Windows, it is straightforward to install Cn3D for both Netscape Navigator and Internet Explorer.
• On Macintosh OS X, installation is a bit more complex. NCBI recommends the following steps for Netscape:
  • Rename or delete the file named "com.netscape.mozilla.plist".
  • Download and extract Cn3D.
  • Select Netscape Menu -> Preferences -> Navigator -> Helper Applications -> New type.
  • Fill in the following fields:
    • Description = "NCBI STRUCTURES"
    • Extension "cgi"
    • MIME "chemical/ncbi-sn1-binary"
  • Application - browse to select the downloaded Cn3D executable.
  • Click OK.
  • After first download of a 3D molecule structure, de-select "always ask" in dialogue box.

Install GO Database and Association Enhancements Locally :

When you download GoMiner, it is configured to query a database hosted on the GoMiner site. You may wish to run a copy of the database for performance or for data customization. For example, one particular customization that we have made available is a feature that enhances the gene term associations for human data. If you want to install a local database follow these installation instructions.

We would like to hear from you. You can reach the team via email.

GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

Notice and Disclaimer