Apache Taverna was an

open source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open ...

tool for designing and executing

workflow A workflow consists of an orchestrated and repeatable pattern 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 sequence of ...

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 e-laboratories and have been used in domains as diverse as systems biol ...

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

Apache incubator Apache Incubator is the gateway for open-source projects intended to become fully fledged Apache Software Foundation projects. The Incubator project was created in October 2002 to provide an entry path to the Apache Software Foundation for projec ...

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

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 ...

SOAP or REST Web services, such as those provided by the

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States 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 ...

, 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 Well ...

, the DNA Databank of Japan (DDBJ), SoapLab,

BioMOBY BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies. BioMOBY is released under the Artistic ...

and

EMBOSS EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of ...

. 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 that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

cheminformatics Cheminformatics (also known as chemoinformatics) refers to 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 problem ...

medicine Medicine is the science and practice of caring for a patient, managing the diagnosis, prognosis, prevention, treatment, palliation of their injury or disease, and promoting their health. Medicine encompasses a variety of health care pract ...

astronomy Astronomy () is a natural science that studies astronomical object, celestial objects and phenomena. It uses mathematics, physics, and chemistry in order to explain their origin and chronology of the Universe, evolution. Objects of interest ...

social science Social science is one of the branches of science, devoted to the study of societies and the relationships among individuals within those societies. The term was formerly used to refer to the field of sociology, the original "science of soc ...

music Music is generally defined as the art of arranging sound to create some combination of form, harmony, melody, rhythm or otherwise expressive content. Exact definitions of music vary considerably around the world, though it is an aspect ...

, and

digital preservation In library and archival science, digital preservation is a formal endeavor to ensure that digital information of continuing value remains accessible and usable. It involves planning, resource allocation, and application of preservation methods an ...

. Some of the services for the use in Taverna workflows could be discovered through the

BioCatalogue The BioCatalogue is a curated catalogue of Life Science Web Services. The BioCatalogue was launched in June 2009 at the Intelligent Systems for Molecular Biology Conference. The project is a collaboration between the myGrid project at the Unive ...

- 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 workfl ...

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 inte ...

site for scientists.

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 of a fatty acid used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are use ...

REST Rest or REST may refer to: Relief from activity * Sleep ** Bed rest * Kneeling * Lying (position) * Sitting * Squatting position Structural support * Structural support ** Rest (cue sports) ** Armrest ** Headrest ** Footrest Arts and entert ...

Web services, and more specific SADI, BioMart,

BioMoby BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies. BioMOBY is released under the Artistic ...

and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on local and remote machines (via

ssh The Secure Shell Protocol (SSH) is a cryptographic network protocol for operating network services securely over an unsecured network. Its most notable applications are remote login and command-line execution. SSH applications are based on ...

), 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) and can be used to compute values (e.g., strings, numbers, or Boolean v ...

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 (from the French ''provenir'', 'to come from/forth') 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 i ...

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 and led by Tim Berners-Lee, the consortium is made up of member organizations that maintain full-time staff working to ...

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

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 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), an island off Malakula Islan ...

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 interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and pro ...

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 The OnlineHPC was a free public web service that supplied tools to deal with high performance computers and online workflow editor. OnlineHPC allowed users to design and execute workflows using the online workflow designer and to work with high per ...

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

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.

External links

Apache Taverna
at the

Taverna
homepage (archive pre-Apache)

References

{{Apache Software Foundation

Taverna A taverna (Greek: ταβέρνα) 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 establishmen ...

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