The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

Abstract

The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.

Figure 1.

The Blast_Align_and_Tree workflow is an example Taverna workflow (available from http://www.myexperiment.org/workflows/3369.html), which performs a phylogenetic analysis. From an input protein sequence, it performs a similarity search against the Uniprot Database (10), using BLAST (11) and aligns similar sequences using ClustalW (12).The alignment is then used to construct a phylogenetic tree, using the EBI ClustalW phylogeny service. The workflow shows 1A = WSDL Web Services, 1B = REST Web Service, 1C = Shim service, 1D = nested workflows (both expanded and collapsed), 1E = asynchronous service looping.