Apache Taverna was an

open source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

tool for designing and executing

workflow Workflow is a generic term for orchestrated and repeatable patterns of activity, enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a seque ...

s, initially created by the

myGrid The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of eScience, e-laboratories and have been used in domains as diverse as sys ...

project under the name ''Taverna Workbench'', then a project under the

Apache Software Foundation The Apache Software Foundation ( ; ASF) is an American nonprofit corporation (classified as a 501(c)(3) organization in the United States) to support a number of open-source software projects. The ASF was formed from a group of developers of the ...

incubator. Taverna allowed users to integrate many different software components, including

web service A web service (WS) is either: * a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or * a server running on a computer device, listening for requests at a particular port over a n ...

s, such as those provided by the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is lo ...

, the

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...

, the

DNA Data Bank of Japan The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Da ...

(DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench. 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 Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

cheminformatics Cheminformatics (also known as chemoinformatics) refers to the use of physical chemistry theory with computer and information science techniques—so called "'' in silico''" techniques—in application to a range of descriptive and prescriptive ...

medicine Medicine is the science and Praxis (process), practice of caring for patients, managing the Medical diagnosis, diagnosis, prognosis, Preventive medicine, prevention, therapy, treatment, Palliative care, palliation of their injury or disease, ...

astronomy Astronomy is a natural science that studies celestial objects and the phenomena that occur in the cosmos. It uses mathematics, physics, and chemistry in order to explain their origin and their overall evolution. Objects of interest includ ...

social science Social science (often rendered in the plural as the social sciences) is one of the branches of science, devoted to the study of societies and the relationships among members within those societies. The term was formerly used to refer to the ...

music Music is the arrangement of sound to create some combination of Musical form, form, harmony, melody, rhythm, or otherwise Musical expression, expressive content. Music is generally agreed to be a cultural universal that is present in all hum ...

, and

digital preservation In library science, library and archival science, digital preservation is a formal process to ensure that digital information of continuing value remains accessible and usable in the long term. It involves planning, resource allocation, and appli ...

. 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 myExperiment is a social web site for researchers sharing research objects such as scientific workflows. The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workf ...

social web The social web is a set of social relations that link people through the World Wide Web. The social web encompasses how websites and software are designed and developed in order to support and foster social interaction. These online social int ...

site for scientists. BioCatalogue and

are another two product from the

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.

Capabilities

Taverna workflows can invoke general

SOAP Soap is a salt (chemistry), salt of a fatty acid (sometimes other carboxylic acids) used for cleaning and lubricating products as well as other applications. In a domestic setting, soaps, specifically "toilet soaps", are surfactants usually u ...

WSDL The Web Services Description Language (WSDL ) is an XML-based interface description language that is used for describing the functionality offered by a web service. The acronym is also used for any specific WSDL description of a web service (also ...

REST REST (Representational State Transfer) is a software architectural style that was created to describe the design and guide the development of the architecture for the World Wide Web. REST defines a set of constraints for how the architecture of ...

Web service A web service (WS) is either: * a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or * a server running on a computer device, listening for requests at a particular port over a n ...

s, 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 XPath (XML Path Language) is an expression language designed to support the query or transformation of XML documents. It was defined by the World Wide Web Consortium (W3C) in 1999, and can be used to compute values (e.g., strings, numbers, or ...

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 Provenance () is the chronology of the ownership, custody or location of a historical object. The term was originally mostly used in relation to works of art, but is now used in similar senses in a wide range of fields, including archaeology, p ...

of the data produced, exposing details of the workflow run as a

W3C The World Wide Web Consortium (W3C) is the main international standards organization for the World Wide Web. Founded in 1994 by Tim Berners-Lee, the consortium is made up of member organizations that maintain full-time staff working together in ...

PROV-O RDF provenance graph, within a structured Research Object bundle ZIP file that includes inputs, outputs, intermediate values and the executed workflow definition; together this format is called ''TavernaProv''. 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

Web Service A web service (WS) is either: * a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or * a server running on a computer device, listening for requests at a particular port over a n ...

description or entered as a

URI Uri may refer to: Places * Canton of Uri, a canton in Switzerland * Úri, a village and commune in Hungary * Uri, Iran, a village in East Azerbaijan Province * Uri, Jammu and Kashmir, a town in India * Uri (island), off Malakula Island in V ...

pattern. Taverna also includes the capability to search for workflows on

. 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 A command-line interface (CLI) is a means of interacting with software via command (computing), commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user ...

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. 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.

Open source community

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

References

{{Apache Software Foundation

Taverna A taverna (; ) is a small Greek restaurant that serves Greek cuisine. The taverna is an integral part of Greek culture and has become familiar to people from other countries who visit Greece, as well as through the establishment of tavernes ...

Bioinformatics software Workflow applications Science and technology in Greater Manchester Department of Computer Science, University of Manchester Software using the Apache license