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

By K. Wolstencroft, R. Haines, Donal K. Fellows, Alan R. Williams, D. Withers, S. Owen, S. Soiland-Reyes, I. Dunlop, A. Nenadic, Paul Fisher and 8 more. Nucleic Acids Res., 2013

769 citations recorded by the source corpus.

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.

Subfields: Information Systems and Management, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/a0b789d1f3afe9cf6fadfaa8f120479181f0c4e5

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Citations in the corpus

ChEMBL web services: streamlining access to drug discovery data and utilities (2015, methodology): “The ChEMBL web services can be called via any programming language or workflow tool, such as Taverna (13), KNIME (14) or Pipeline Pilot (http://www.”
High-Content Screening for Quantitative Cell Biology. (2016, neutral): “Taverna Domain-independent workflow management system [80] www.”
BioContainers: an open-source and community-driven framework for software standardization (2017, methodology): “…have been moved from single and individual tools to complex and integrated workflow systems such as OpenMS (Ro¨st et al. , 2016), Taverna (Wolstencroft et al. , 2013) and Galaxy (Afgan et al. , 2016), creating two major challenges for software developers and the bioinformatics…”
Cytoscape Automation: empowering workflow-based network analysis (2019, methodology): “Finally, as an interactive tool, Cytoscape is not positioned to add value to emerging workflows that integrate one or more external data acquisition and analysis tools (e.g., Galaxy [2], Taverna [3], and libraries provided in repositories such as PyPI [4] and Bioconductor [5]).”
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, methodology): “The TPP has been adapted [26] to the Taverna [42] workflow platform, as well as others.”
A Survey of Data-Intensive Scientific Workflow Management (2015, methodology): “The workflows designed through Taverna can be shared through “myExperiment” social network [136].”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016, methodology): “Early platforms for doing genome analyses in a Web browser include Taverna (4,5), GenePattern (6) and Galaxy.”
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers (2014, methodology): “The Connectivity Search web services can be called via any programming language or workflow tool, such as Taverna [15,16], KNIME [17,18], or Pipeline Pilot [19].”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, background): “Many of these features have existed in in standalone workflow systems, such as Taverna (31), for sometime, but have been widely requested by Galaxy users.”
Canadian Association of Radiologists White Paper on Artificial Intelligence in Radiology (2018, background): “Semantic Web Technologies and RESTful web service frameworks may be harnessed for this purpose in a manner similar to that implemented in existing integrative biomedical informatics frameworks [48].”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “, 2010], Taverna [Wolstencroft et al., 2013], and Anduril [Ovaska et al.”