Microsoft Word add-in for the GenePattern Reproducible Research Document (GRRD)
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.
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.