Microsoft Word add-in for the GenePattern Reproducible Research Document

Source code checked in, #69631

Project Collection Service Accounts — Mon, 01 Oct 2012 21:13:48 GMT

Upgrade: New Version of LabDefaultTemplate.xaml. To upgrade your build definitions, please visit the following link: http://go.microsoft.com/fwlink/?LinkId=254563

Source code checked in, #69630

Project Collection Service Accounts — Mon, 01 Oct 2012 21:07:03 GMT

Checked in by server upgrade

Created Issue: Addin only works in Word 2007 [9625]

BarbaraHill — Thu, 06 Sep 2012 14:32:59 GMT

From the GenePattern development team.

Please note that the add-in will only work in Word 2007. It is not compatible with Word 2010.

Created Issue: Tab does not appear in MS Word 2007 [7134]

rakbani — Thu, 19 Aug 2010 21:15:59 GMT

Hi. I tried installing the add-in and the prerequisite Microsoft VSTO 2005 software and the installation was successful. However, the GenePattern tab does not appear in Word. I followed all the steps in the troubleshooting guide, including uninstalling, reinstalling, restarting etc. but to no avail. I tried manually enabling the COM Add-in under Word 2007 according to the troubleshooting guide, but I get the following error message under Load Behavior: "Not loaded. A runtime error occurred during the loading of the COM Add-in." I tried installing on a completely separate system too (my laptop), and exactly the same thing happens. Please help. Here are my system details:

Desktop:
OS: Windows XP Pro, version 2002, SP3, 32-bit
Processor: Intel Core2 Duo
RAM: 4 GB
MS Office Enterprise 2007: Word 2007 (12.0.6541.5000) SP2 MSO (12.0.6535.5002)
Microsoft Visual Studio 2005 Tools for Office Second Edition Runtime (VSTO 2005 SE) (x86)

Laptop:
OS: Windows 7 Pro, 64-bit
Processor: Intel Core i7
RAM: 4 GB
MS Office Enterprise 2007: Word 2007 (12.0.6541.5000) SP2 MSO (12.0.6535.5002)
Microsoft Visual Studio 2005 Tools for Office Second Edition Runtime (VSTO 2005 SE) (x86)

Source code checked in, #48968

_TFSSERVICE — Thu, 22 Jul 2010 18:55:41 GMT

Checked in by server upgrade

Project License Changed

Thu, 25 Feb 2010 01:35:34 GMT

Microsoft Platform and Application License This license governs use of the accompanying software. If you use the software, you accept this license. If you do not accept the license, do not use the software. 1. Definitions The terms “reproduce,” “reproduction,” “derivative works,” and “distribution” have the same meaning here as under U.S. copyright law. A “contribution” is the original software, or any additions or changes to the software. A “contributor” is any person that distributes its contribution under this license. “Licensed patents” are a contributor’s patent claims that read directly on its contribution. 2. Grant of Rights (A) Copyright Grant- Subject to the terms of this license, including the license conditions and limitations in section 3, each contributor grants you a non-exclusive, worldwide, royalty-free copyright license to reproduce its contribution, prepare derivative works of its contribution, and distribute its contribution or any derivative works that you create. (B) Patent Grant- Subject to the terms of this license, including the license conditions and limitations in section 3, each contributor grants you a non-exclusive, worldwide, royalty-free license under its licensed patents to make, have made, use, sell, offer for sale, import, and/or otherwise dispose of its contribution in the software or derivative works of the contribution in the software. 3. Conditions and Limitations (A) No Trademark License- This license does not grant you rights to use any contributors’ name, logo, or trademarks. (B) If you bring a patent claim against any contributor over patents that you claim are infringed by the software, your patent license from such contributor to the software ends automatically. (C) If you distribute any portion of the software, you must retain all copyright, patent, trademark, and attribution notices that are present in the software. (D) If you distribute any portion of the software in source code form, you may do so only under this license by including a complete copy of this license with your distribution. If you distribute any portion of the software in compiled or object code form, you may only do so under a license that complies with this license. (E) The software is licensed “as-is.” You bear the risk of using it. The contributors give no express warranties, guarantees or conditions. You may have additional consumer rights under your local laws which this license cannot change. To the extent permitted under your local laws, the contributors exclude the implied warranties of merchantability, fitness for a particular purpose and non-infringement. (F) Platform Limitation- The licenses granted in sections 2(A) & 2(B) extend only to the software or derivative works that you create that (1) run on a Microsoft Windows operating system product, and also (2) operate with Microsoft Office productivity applications.

Source code checked in, #37113

BroadGenePattern — Mon, 22 Feb 2010 20:55:13 GMT

Updated source with namespace changes, reference to Office 3.0 runtime, EULA, bug fixes

Source code checked in, #37109

BroadGenePattern — Mon, 22 Feb 2010 19:40:13 GMT

Deleting old set for adding updated source

Updated Release: Setup and Documentation (Jan 22, 2010)

BroadGenePattern — Fri, 12 Feb 2010 19:47:18 GMT

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:

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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:

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Released: Setup and Documentation (Jan 22, 2010)

Fri, 12 Feb 2010 19:47:18 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Updated Wiki: Home

BroadGenePattern — Fri, 22 Jan 2010 18:12:15 GMT

Project Description
The GenePattern computational biology software provides a way to create analytic workflows (pipelines) enabling in silico reproducible research. This Word 2007 add-in supports embedding pipelines in a document and rerunning them on any GenePattern server from the Word application.

Credits
GenePattern is a development project at the Broad Institute of MIT and Harvard. Development of the GRRD was funded by Microsoft and implemented by Infusion and Persistent Systems Ltd.

Updated Wiki: Home

BroadGenePattern — Fri, 22 Jan 2010 18:09:53 GMT

Updated Wiki: Home

BroadGenePattern — Fri, 22 Jan 2010 18:09:35 GMT

Updated Release: Setup and Documentation (Jan 22, 2010)

BroadGenePattern — Fri, 22 Jan 2010 15:27:53 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Released: Setup and Documentation (Jan 22, 2010)

Fri, 22 Jan 2010 15:27:53 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Updated Release: Setup and Documentation (Jan 22, 2010)

BroadGenePattern — Fri, 22 Jan 2010 15:20:35 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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 et al., Science 286, 531 (Oct 15, 1999)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Updated Wiki: Home

BroadGenePattern — Fri, 15 Jan 2010 19:46:21 GMT

Updated Wiki: Home

BroadGenePattern — Fri, 15 Jan 2010 18:58:34 GMT

Project Description
The GenePattern computational biology software provides a way to create analytic workflows (pipelines) enabling in silico reproducible research. This Word 2007 add-in supports embedding pipelines in a document and rerunning them on any GenePattern server from the Word application.

Credits
Development of the GRRD was funded by Microsoft and implemented by Infusion and Persistent IT Solutions.

Updated Release: Setup and Documentation (Jul 16, 2009)

BroadGenePattern — Tue, 17 Nov 2009 18:24:16 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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 et al., Science 286, 531 (Oct 15, 1999)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.

Released: Setup and Documentation (Jul 16, 2009)

Tue, 17 Nov 2009 18:24:16 GMT

Download and install pre-requisite Office-related software from http://www.microsoft.com/DOWNLOADS/details.aspx?FamilyID=54eb3a5a-0e52-40f9-a2d1-eecd7a092dcb.
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 et al., Science 286, 531 (Oct 15, 1999)

Download the updated authentication library from ftp://ftp.broadinstitute.org/pub/genepattern/src/gp-custom-auth.jar
Add that library to the classpath for the gp web application; for example, <GenePatternServer>/Tomcat/webapps/gp/WEB-INF/lib
Make sure the following entry is in the genepattern.properties file: authentication.class=org.genepattern.server.auth.plugin.GenePatternAuthenticationUpdate02
Restart your server.

For details on modifying GenePattern authentication, see the GenePattern documentation.