Taverna workbench

Draft

Introduction

“Taverna is an open source family of tools for designing and executing workflows, created by the myGrid project and funded by OMII UK, the EPSRC, BBRC, ESRC, JISC and Microsoft. The workbench includes contributions by the Moby Consortiumm and the University of Twente. The family consists of the Taverna Engine (the workhorse), and the Taverna Workbench (desktop client) that sits on top of the Engine.” (Workflow Type: Taverna 2, myExperiment, retrieved 17:11, 14 June 2010 (UTC))

See also myExperiment (a repository for scientific workflows and other objects. It is integrated with the taverna workbench).

Architecture

Taverna defines its own workflow definition language. It “is designed to present a workflow model where entities within the workflow map as far as is possible onto entities within a scientist’s description of the eScience process the workflow defines. This leads to a dataflow view of the world – the workflow is constructed from data processing and data transport (processors and data links)”. In contrast, BPEL for example, “is a process-centric model where the nodes in the workflows are activities and the data passed between them form a control system rather than being a genuine flow of messages.” (Why Taverna does not use BPEL as the workflow definition language?, retrieved 17:11, 14 June 2010 (UTC))

Examples

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Source: http://www.myexperiment.org/workflows/821

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/. Source: http://www.myexperiment.org/workflows/824

Links

• Taverna Workbench (home page, download, documentation, etc.)

References

• Missier, P., Turi, D., Goble, C., Oinn, T. and De Roure, D. (2007) Taverna Workflows: Syntax and Semantics. In: IEEE International Conference on e-Science and Grid Computing, December 2007, Bangalore, India. pp. 441-448.

• Turi. D; P. Missier, C. Goble, D. De Roure, and T. Oinn, "Taverna Workflows: Syntax and Semantics," in IEEE International Conference on e-Science and Grid Computing, 2007, pp. 441-448. PDF

• Oinn, Tom et al. (2000). Taverna: Lessons in creating a workflow environment for the life sciences, Concurrency Computat.: Pract. Exper. 1-7. PDF Reprint.

• Wei Tan, Paolo Missier, Ravi Madduri and Ian Foster. Building Scientific Workflow with Taverna and BPEL: a Comparative Study in caGrid. Proc. 3rd e-Science Conference. 2007. PDF Preprint.