Microsoft Word add-in for the
GenePattern Reproducible Research Document (GRRD)
Description
To facilitate publishing reproducible results, scientists need a simple way of capturing computational workflows and embedding them into papers.
GenePattern automatically captures the history of any computational work being done, allowing scientists to easily generate pipelines to reproduce computational methods. Now researchers at Microsoft® and the Broad have collaborated to create the Microsoft Word 2007 add-in for the GenePattern Reproducible Research Document (GRRD), which allows scientists to embed their pipelines in a Word document.
Using the add-in, readers of the document can rerun the pipelines on any GenePattern server from within the Word application.
Users who do not have access to Microsoft Word 2007 can use the GenePatternDocumentExtractor module to extract GenePattern pipelines and data from a Word document.
References
- Accessible Reproducible Research by Jill P. Mesirov (Science, 327:415, 2010).
- The User Manual (Word document) 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 Golub & Slonim et al. (Science, 286:531, 1999) 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.
How to install the add-in
Prerequisites: The add-in is compatible with Word 2007. It has been tested on platforms that run the native Windows operating system, Windows installed on Parallels and Windows installed on VMWare virtualization software.
To install the add-in into Microsoft Office:
- Navigate to the codeplex site for the add-in: http://genepatternwordaddin.codeplex.com/
- Click the Downloads tab.
- Download and install pre-requisite Office-related software from here.
- 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 GRRD User Manual.
For assistance with the add-in, please use the Discussions and Issue Tracker links provided on the codeplex site.
Credits
Development of the GRRD was funded by Microsoft and implemented by Infusion and Persistent Systems, Ltd.
