Apache Taverna

Apache Taverna

Taverna Workbench
Developer(s) Apache Software Foundation (myGrid for 2.x)
Stable release 2.5 / April 16, 2014 (2014-04-16)
Development status Active
Written in Java
Operating system Linux, Mac OS X, Microsoft Windows
Type Scientific workflow system
License Apache License 2.0 (LGPL for 2.x)
Website taverna.incubator.apache.org

Apache Taverna is an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, now a project under the Apache incubator. Taverna allows 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 is not finite and users can import new service descriptions into the Taverna Workbench.[1][2][3][4][5][6][7][8]

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

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

Taverna is 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.

Capabilities

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,[14] within a structured Research Object bundle[15] ZIP file that includes inputs, outputs, intermediate values and the executed workflow definition.[16]

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:

Taverna allows pipelining and streaming of data.[17] 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.[18]

Taverna Workbench 2.1 splash screen

Open source community

Taverna has been an open-source project since 2003,[19] with contributors from multiple academic and industry institutions. In 2014-10, Taverna became an independent Apache incubator project,[20] and changed name to Apache Taverna (incubating). The project is developing Apache Taverna 3.x,[21] which license change from LGPL 2.1 to Apache License 2.0.

External links

References

  1. ↑ Belhajjame, K.; Wolstencroft, K.; Corcho, O.; Oinn, T.; Tanoh, F.; William, A.; Goble, C. (2008). "Metadata Management in the Taverna Workflow System": 651–656. doi:10.1109/CCGRID.2008.17.
  2. ↑ Li, P.; Castrillo, J. I.; Velarde, G.; Wassink, I.; Soiland-Reyes, S.; Owen, S.; Withers, D.; Oinn, T.; Pocock, M. R.; Goble, C. A.; Oliver, S. G.; Kell, D. B. (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.; Carver, T.; Glover, K.; Pocock, M. R.; Wipat, A.; Li, P. (2004). "Taverna: A tool for the composition and enactment of bioinformatics workflows". Bioinformatics 20 (17): 3045–3054. doi:10.1093/bioinformatics/bth361. PMID 15201187.
  4. ↑ Oinn, T.; Greenwood, M.; Addis, M.; Alpdemir, M. N.; Ferris, J.; Glover, K.; Goble, C.; Goderis, A.; Hull, D.; Marvin, D.; Li, P.; Lord, P.; Pocock, M. R.; Senger, M.; Stevens, R.; Wipat, A.; Wroe, C. (2006). "Taverna: Lessons in creating a workflow environment for the life sciences". Concurrency and Computation: Practice and Experience 18 (10): 1067–1100. doi:10.1002/cpe.993.
  5. ↑ Hull, D.; Wolstencroft, K.; Stevens, R.; Goble, C. A.; Pocock, M. R.; Li, P.; Oinn, T. (2006). "Taverna: A tool for building and running workflows of services". Nucleic Acids Research 34 (Web Server issue): W729–W732. doi:10.1093/nar/gkl320. PMC 1538887. PMID 16845108.
  6. ↑ Kawas, E.; Senger, M.; Wilkinson, M. D. (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, A. (2006). "XQTav: An XQuery processor for Taverna environment". Bioinformatics 22 (10): 1280–1281. doi:10.1093/bioinformatics/btl101. PMID 16551662.
  8. ↑ Wolstencroft, K.; Haines, R.; Fellows, D.; Williams, A.; Withers, D.; Owen, S.; Soiland-Reyes, S.; Dunlop, I.; Nenadic, A.; Fisher, P.; Bhagat, J.; Belhajjame, K.; Bacall, F.; Hardisty, A.; Nieva De La Hidalga, A.; Balcazar Vargas, M. P.; Sufi, S.; Goble, C. (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–W561. doi:10.1093/nar/gkt328. PMC 3692062. PMID 23640334.
  9. ↑ Stevens, R. D.; Robinson, A. J.; Goble, C. A. (2003). "MyGrid: Personalised bioinformatics on the information grid". Bioinformatics 19: i302–i304. doi:10.1093/bioinformatics/btg1041. PMID 12855473.
  10. ↑ Stevens, R. D.; Tipney, H. J.; Wroe, C. J.; Oinn, T. M.; Senger, M.; Lord, P. W.; Goble, C. A.; Brass, A.; Tassabehji, M. (2004). "Exploring Williams-Beuren syndrome using myGrid". Bioinformatics 20: i303–i310. doi:10.1093/bioinformatics/bth944. PMID 15262813.
  11. ↑ Truszkowski, A.; Jayaseelan, K.; Neumann, S.; Willighagen, E. L.; Zielesny, A.; Steinbeck, C. (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, R. N.; Romaniello, M.; Ullgrén, M.; Järveläinen, P.; Maisala, S.; Oittinen, T.; Savolainen, V.; Solin, O.; Tyynelä, J.; Peron, M.; Izzo, C.; Licha, T. (2008). "ESO Reflex: A Graphical Workflow Engine for Running Recipes". The 2007 ESO Instrument Calibration Workshop. ESO Astrophysics Symposia European Southern Observatory. p. 169. 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 execution" (PDF).
  14. ↑ 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.
  15. ↑ Soiland-Reyes, S; Gamble, M; Haines, R (2014-11-05). "Research Object Bundle 1.0" (Specification). researchobject.org. Zenodo. doi:10.5281/zenodo.12586. Retrieved 28 January 2015.
  16. ↑ Soiland-Reyes, S; Nenadic, A (2014-10-21). "taverna-prov: Structure of exported provenance". GitHub. Archived from the original on 2014-10-21. Retrieved 28 January 2015.
  17. ↑ "Implicit iteration". Taverna 2.5 User Manual. myGrid. 2014-09-09. Retrieved 28 January 2015.
  18. ↑ Soiland-Reyes, Stian (2010-12-13). "Parallel service invocations". The Taverna Knowledge Blog. knowledgeblog.org. Retrieved 28 January 2015.
  19. ↑ Soiland-Reyes, S; Sufi, S; Seaborne, S (2014-09-23). "Taverna Proposal". Incubator Wiki. Apache Software Foundation. Retrieved 28 January 2015.
  20. ↑ "Taverna Project Incubation Status". Apache Incubator. Apache Software Foundation. Retrieved 28 January 2015.
  21. ↑ "Download Apache Taverna". Apache Software Foundation. Retrieved 28 January 2015.
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