Setup and Documentation

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Released: Jan 22, 2010
Updated: Feb 12, 2010 by BroadGenePattern
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Release Notes

The GenePatternAddIn setup program will install the add-in into Microsoft Office. The add-in is compatible with Word 2007 but not earlier versions. It has been tested on platforms that run the native Windows operating system or that run Windows using the VMware virtualization software.

To install the add-in:
  1. Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
  2. Run the GenePatternAddIn setup program to install the add-in into Microsoft Office. If the installation is not successful, see the Troubleshooting section of the User Manual.

For information about the add-in:
  • The User Manual describes how to install and use the GenePattern Reproducible Research Document add-in.
  • The Example User Session is a short QuickTime movie that demonstrates a simple scenario.
  • The Sample Add-in Document is an excerpt from our 1999 paper [1] on the classification of leukemia recreated with Microsoft Word and the GenePattern Reproducible Research Document add-in. We linked GenePattern pipelines that encapsulate the methods and original data described in the paper. The document contains a total of six pipeline associations, representing the analyses behind the prediction results in Table 1, the neighborhood analysis in Figure 2, the prediction strengths in Figure 3a, and the genes distinguishing two types of acute leukemia in Figure 3b. Note that these pipelines were produced some time after the paper was published, and are not the original code used prepublication. They may differ somewhat in detail but do yield the same overall results. We also note here that each association took only a few minutes to complete. References: 1.T. R. Golub & Slonim et al., Science 286, 531 (Oct 15, 1999)


WARNING: GenePattern 3.2 servers that were installed between 22 June 2009 and 23 July 2009 (builds 8538 and 8571) require a patch to allow full use of the add-in. You may either reinstall the server using build 8577 from http://genepattern.broadinstitute.org/gp/installer/install.htm or update the authentication library as follows:
  1. Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
  2. Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
  3. Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
  4. Restart your server.
For details on modifying GenePattern authentication, see the GenePattern documentation.

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