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Apache Taverna

Summary

Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, then a project under the Apache incubator. Taverna allowed users to integrate many different software components, including WSDL SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench.[1][2][3][4][5][6][7][8]

Apache Taverna
Developer(s)Apache Software Foundation (myGrid for 2.x)
Stable release
3.1 / July 1, 2016; 8 years ago (2016-07-01)
Repository
  • git-wip-us.apache.org/repos/asf/incubator-taverna-commandline.git Edit this at Wikidata
Written inJava
Operating systemLinux, Mac OS X, Microsoft Windows
TypeScientific workflow system
LicenseApache License 2.0 (LGPL for 2.x)
Websitetaverna.incubator.apache.org

Taverna Workbench provided a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow engine was also available separately, as a Java API, command line tool or as a server.

Taverna was used by users in many domains, such as bioinformatics,[9][10] cheminformatics,[11] medicine, astronomy,[12] social science, music, and digital preservation.[13]

Some of the services for the use in Taverna workflows could be discovered through the BioCatalogue - a public, centralised and curated registry of Life Science Web services. Taverna workflows could also be shared with other people through the myExperiment social web site for scientists.[14] BioCatalogue and myExperiment are another two product from the myGrid consortium.

Taverna was used in over 350 organizations around the world, both academic and commercial. As of 2011, there have been over 80,000 downloads of Taverna across different versions.

On February 20, 2020, Apache Incubator retired the project and removed the code from its website.[15]

Capabilities

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Taverna workflows can invoke general SOAP/WSDL or REST Web services, and more specific SADI, BioMart, BioMoby and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on local and remote machines (via ssh), do XPath and other text manipulation, import a spreadsheet and include sub-workflows.

Taverna Workbench includes the ability to monitor the running of a workflow and to examine the provenance of the data produced, exposing details of the workflow run as a W3C PROV-O RDF provenance graph,[16] within a structured Research Object bundle[17] ZIP file that includes inputs, outputs, intermediate values and the executed workflow definition; together this format is called TavernaProv.[18]

Taverna includes the ability to search for services described in BioCatalogue to invoke from workflows. However, services do not need to be described within BioCatalogue to be included in workflows as they can be added from a WSDL Web Service description or entered as a REST URI pattern.

Taverna also includes the capability to search for workflows on myExperiment. The Taverna Workbench can download, modify and run workflows discovered on myExperiment, and also upload created workflows in order to share them with others using the social aspects of myExperiment.

Taverna workflows do not need to be executed within the Taverna Workbench. Workflows can also be run by:

  • a command line execution tool
  • remote execution server that allow Taverna workflows to be run on other machines, on computational grids, clouds, from Web pages and portals
  • online workflow designer and enactor OnlineHPC

Taverna allows pipelining and streaming of data.[19] This means that services downstream in the workflow can start as soon as the first data item is received, without waiting for the whole data list to become available from upstream services and iterations. Taverna services execute in parallel when possible, as Taverna workflows are primarily data-driven rather than control-driven.[20]

 
Taverna Workbench 2.1 splash screen

Open source community

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Taverna has been an open-source project since 2003,[21] with contributors from multiple academic and industry institutions. In October 2014 Taverna became an independent Apache incubator project,[15] and changed its name to Apache Taverna (incubating). The project is developing Apache Taverna 3.x,[22] which license changed from LGPL 2.1 to Apache License 2.0.

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  • Apache Taverna at the Apache incubator
  • Taverna homepage (archive pre-Apache)

References

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  1. ^ Belhajjame K, Wolstencroft K, Corcho O, Oinn T, Tanoh F, William A, Goble C (2008). "Metadata Management in the Taverna Workflow System". 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (CCGRID). pp. 651–656. doi:10.1109/CCGRID.2008.17. ISBN 9780769531564. S2CID 9996653.
  2. ^ Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, et al. (August 2008). "Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data". BMC Bioinformatics. 9: 334. doi:10.1186/1471-2105-9-334. PMC 2528018. PMID 18687127.
  3. ^ Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, et al. (November 2004). "Taverna: a tool for the composition and enactment of bioinformatics workflows". Bioinformatics. 20 (17): 3045–54. doi:10.1093/bioinformatics/bth361. PMID 15201187.
  4. ^ Oinn T, Greenwood M, Addis M, Alpdemir MN, Ferris J, Glover K, et al. (2006). "Taverna: Lessons in creating a workflow environment for the life sciences" (PDF). Concurrency and Computation: Practice and Experience. 18 (10): 1067–1100. doi:10.1002/cpe.993. S2CID 10219281.
  5. ^ Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T (July 2006). "Taverna: a tool for building and running workflows of services". Nucleic Acids Research. 34 (Web Server issue): W729-32. doi:10.1093/nar/gkl320. PMC 1538887. PMID 16845108.  
  6. ^ Kawas E, Senger M, Wilkinson MD (November 2006). "BioMoby extensions to the Taverna workflow management and enactment software". BMC Bioinformatics. 7: 523. doi:10.1186/1471-2105-7-523. PMC 1693925. PMID 17137515.
  7. ^ Sroka J, Kaczor G, Tyszkiewicz J, Kierzek AM (May 2006). "XQTav: an XQuery processor for Taverna environment". Bioinformatics. 22 (10): 1280–1. doi:10.1093/bioinformatics/btl101. PMID 16551662.
  8. ^ Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, et al. (July 2013). "The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud". Nucleic Acids Research. 41 (Web Server issue): W557-61. doi:10.1093/nar/gkt328. PMC 3692062. PMID 23640334.
  9. ^ Stevens RD, Robinson AJ, Goble CA (2003). "myGrid: personalised bioinformatics on the information grid". Bioinformatics. 19 (Suppl 1): i302-4. doi:10.1093/bioinformatics/btg1041. PMID 12855473.
  10. ^ Stevens RD, Tipney HJ, Wroe CJ, Oinn TM, Senger M, Lord PW, et al. (August 2004). "Exploring Williams-Beuren syndrome using myGrid". Bioinformatics. 20 (Suppl 1): i303-10. doi:10.1093/bioinformatics/bth944. PMID 15262813.
  11. ^ Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A, Steinbeck C (December 2011). "New developments on the cheminformatics open workflow environment CDK-Taverna". Journal of Cheminformatics. 3: 54. doi:10.1186/1758-2946-3-54. PMC 3292505. PMID 22166170.
  12. ^ Hook RN, Romaniello M, Ullgrén M, Järveläinen P, Maisala S, Oittinen T, et al. (2008). "ESO Reflex: A Graphical Workflow Engine for Running Recipes". The 2007 ESO Instrument Calibration Workshop. ESO Astrophysics Symposia European Southern Observatory. pp. 169–175. doi:10.1007/978-3-540-76963-7_23. ISBN 978-3-540-76962-0.
  13. ^ Raditsch M, Schlarb S, Møldrup-Dalum P, Medjkoune L (2012). "Web content executable workflows for experimental executio" (PDF).
  14. ^ Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, et al. (July 2010). "myExperiment: a repository and social network for the sharing of bioinformatics workflows". Nucleic Acids Research. 38 (Web Server issue): W677-82. doi:10.1093/nar/gkq429. PMC 2896080. PMID 20501605.
  15. ^ a b "Taverna Project Incubation Status". Apache Incubator. Apache Software Foundation. Retrieved 28 January 2015.
  16. ^ Belhajjame K, Zhao J, Garijo D, Garrido A, Soiland-Reyes S, Alper P, Corcho O (2013). "A workflow PROV-corpus based on Taverna and Wings". Proceedings of the Joint EDBT/ICDT 2013 Workshops on - EDBT '13. p. 331. doi:10.1145/2457317.2457376. ISBN 9781450315999.
  17. ^ Soiland-Reyes S, Gamble M, Haines R (5 November 2014). "Research Object Bundle 1.0" (Specification). researchobject.org. doi:10.5281/zenodo.12586. Retrieved 28 January 2015.
  18. ^ Soiland-Reyes, Stian; Alper, Pinar; Goble, Carole (11 May 2016). "Tracking workflow execution with TavernaProv". zenodo.org. doi:10.5281/zenodo.51314.
  19. ^ "Implicit iteration". Taverna 2.5 User Manual. myGrid. 9 September 2014. Archived from the original on 22 March 2015. Retrieved 28 January 2015.
  20. ^ Soiland-Reyes S (13 December 2010). "Parallel service invocations". The Taverna Knowledge Blog. knowledgeblog.org. Retrieved 28 January 2015.
  21. ^ Soiland-Reyes S, Sufi S, Seaborne S (23 September 2014). "Taverna Proposal". Incubator Wiki. Apache Software Foundation. Retrieved 28 January 2015.
  22. ^ "Download Apache Taverna". Apache Software Foundation. Retrieved 28 January 2015.

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