Apache Taverna

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Apache Taverna
Stable release
3.1 / July 1, 2016; 7 years ago (2016-07-01)
Repository
Written in
LGPL for 2.x)
Websitetaverna.incubator.apache.org

Apache Taverna was an

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]

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

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

Taverna workflows can invoke general

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

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

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

Taverna has been an open-source project since 2003,

LGPL 2.1 to Apache License 2.0
.

External links

References

  1. S2CID 9996653
    .
  2. PMID 18687127
    .
  3. PMID 15201187
    .
  4. S2CID 10219281
    .
  5. PMID 16845108. Open access icon
  6. PMID 17137515
    .
  7. PMID 16551662
    .
  8. PMID 23640334
    .
  9. PMID 12855473
    .
  10. PMID 15262813
    .
  11. PMID 22166170
    .
  12. 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. PMID 20501605
    .
  15. ^ a b "Taverna Project Incubation Status". Apache Incubator. Apache Software Foundation. Retrieved 28 January 2015.
  16. ISBN 9781450315999
    .
  17. doi:10.5281/zenodo.12586
    . Retrieved 28 January 2015.
  18. 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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