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Using R in Taverna: RShell v1.2.

Ingo Wassink1, Han Rauwerda, Pieter B T Neerincx

  • 1Human Media Interaction Group, University of Twente, Enschede, The Netherlands. wassinki@ewi.utwente.nl

BMC Research Notes
|July 18, 2009
PubMed
Summary
This summary is machine-generated.

The RShell plugin enhances Taverna workflows by integrating the R statistical language, offering improved data type support, multiple inputs/outputs, and persistent sessions for omics data analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Science

Background:

  • R is a widely used statistical language for omics data analysis.
  • Taverna is an open-source workflow management system.
  • Previous Taverna versions had limited R support, hindering its practical application.

Purpose of the Study:

  • To develop an R plugin for Taverna to enable comprehensive R functionality within workflows.
  • To address limitations in data type support, output configuration, and session management for R in Taverna.

Main Methods:

  • Developed the RShell plugin, directly utilizing the R interpreter.
  • Implemented an RShell Session Manager for R server communication.
  • Designed a configurable Taverna processor for R scripts with multiple inputs/outputs and data type support (strings, numeric, images).

Main Results:

  • RShell supports R versions up to 2.9, persistent sessions, and PDF vector graphics output.
  • Introduced syntax highlighting for R code and improved usability with fewer port types.
  • Demonstrated value through a use-case workflow mapping oligonucleotide probes to the Ensembl genome assembly.

Conclusions:

  • The RShell plugin provides a highly configurable solution for integrating R scripts into Taverna workflows.
  • Enables life scientists to leverage R's statistical capabilities within a workflow management system.