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BMC Research Notes

, 2:138

First Online: 16 July 2009Received: 19 February 2009Accepted: 16 July 2009DOI: 10.1186-1756-0500-2-138

Cite this article as: Wassink, I., Rauwerda, H., Neerincx, P.B. et al. BMC Res Notes 2009 2: 138. doi:10.1186-1756-0500-2-138


BackgroundR is the statistical language commonly used by many life scientists in omics data analysis. At the same time, these complex analyses benefit from a workflow approach, such as used by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical.

FindingsWe have developed an R plugin for Taverna: RShell, which provides R functionality within workflows designed in Taverna. In order to fully support the R language, our RShell plugin directly uses the R interpreter. The RShell plugin consists of a Taverna processor for R scripts and an RShell Session Manager that communicates with the R server. We made the RShell processor highly configurable allowing the user to define multiple inputs and outputs. Also, various data types are supported, such as strings, numeric data and images. To limit data transport between multiple RShell processors, the RShell plugin also supports persistent sessions. Here, we will describe the architecture of RShell and the new features that are introduced in version 1.2, i.e.: i Support for R up to and including R version 2.9; ii Support for persistent sessions to limit data transfer; iii Support for vector graphics output through PDF; ivSyntax highlighting of the R code; v Improved usability through fewer port types.

Our new RShell processor is backwards compatible with workflows that use older versions of the RShell processor. We demonstrate the value of the RShell processor by a use-case workflow that maps oligonucleotide probes designed with DNA sequence information from Vega onto the Ensembl genome assembly.

ConclusionOur RShell plugin enables Taverna users to employ R scripts within their workflows in a highly configurable way.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-2-138 contains supplementary material, which is available to authorized users.

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Author: Ingo Wassink - Han Rauwerda - Pieter BT Neerincx - Paul E van der Vet - Timo M Breit - Jack AM Leunissen - Anton Nijh


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