Taverna workbench
Encyclopedia
Taverna Workbench is an open source software tool for designing and executing workflow
s, created by the myGrid
project and funded through the OMII-UK
. Taverna allows users to integrate many different software components, including SOAP or REST Web service
s, 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.
Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow enactment engine is also available separately, as a command line tool or as a server.
Taverna is used by users in many domains, such as bioinformatics
, cheminformatics
, medicine
, astronomy
, social science
and music
.
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.
and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on 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. The provenance system for Taverna 2.1 is being co-ordinated with the Open Provenance Model.
Taverna includes the ability to search for services described in BioCatalogue
to include within workflows. However, services do not need to be described within BioCatalogue to be included in workflows.
Taverna also includes the capability to search for workflows on myExperiment
. You can download, modify and run the workflows discovered on myExperiment from within the Taverna Workbench. You can also upload you workflows from the Workbench to myExperiment in order to share them with others.
Taverna workflows do not need to be executed within the Taverna Workbench. Workflows can also be run by:
Taverna 2 (the second generation of the Taverna software) allows pipelining and streaming of data. This means that services downstream a workflow can start as soon as the first piece of data is received, without waiting for the whole piece of data to become available. It also has improved memory usage allowing the handling of much larger data sets.
, SADI semantic Web services, and caGrid
. It has also been bundled with other products, for example the Taverna-LC plugin for OpenOffice Calc allows calling services as spreadsheet functions.
Various projects and institutions have run Taverna workflows on grids or have used Taverna to access services on grids, such as KnowARC, NGS (National Grid Service
), EGEE (Enabling Grids for E-sciencE) and caGrid
.
External tools can be included within Taverna workflows either scripts such as Java Beanshell, though the use of an API Consumer service that generates services for the methods exposed by the tool written in Java or via external tools plugin, which allows users to run tools on a grid or remote/local machine using grid or ssh authentication.
Workflow
A workflow consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. Workflow may be seen as any abstraction of real work...
s, created by the myGrid
MyGrid
The myGrid consortium is a multi-institutional, multi-disciplinary internationally leading research group focussing on the challenges of eScience...
project and funded through the OMII-UK
OMII-UK
is an open-source organisation that empowers the UK research community by providing software for use in all disciplines of research. Their mission is to cultivate and sustain community software that is important to research....
. Taverna allows users to integrate many different software components, including SOAP or REST Web service
Web service
A Web service is a method of communication between two electronic devices over the web.The W3C defines a "Web service" as "a software system designed to support interoperable machine-to-machine interaction over a network". It has an interface described in a machine-processable format...
s, such as those provided by the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
, the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
, the DNA Databank of Japan (DDBJ)
DNA Data Bank of Japan
The DNA Data Bank of Japan is a biological database that collects DNA sequences. It is located at the National Institute of Genetics in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC...
, SoapLab
Soaplab
Soaplab is a Web Services software framework specialised for bioinformatics programs with command-line interface. It includes a module for running command-line programs as Web Services jobs and provides support to generate Java Web Services web applications for them. It allows both synchronous and...
, BioMOBY
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.- The BioMOBY project :...
and EMBOSS
EMBOSS
EMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
. The set of available services is not finite and users can import new service descriptions into the Taverna Workbench.
Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow enactment engine is also available separately, as a command line tool or as a server.
Taverna is used by users in many domains, such as bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
, cheminformatics
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
, medicine
Medicine
Medicine is the science and art of healing. It encompasses a variety of health care practices evolved to maintain and restore health by the prevention and treatment of illness....
, astronomy
Astronomy
Astronomy is a natural science that deals with the study of celestial objects and phenomena that originate outside the atmosphere of Earth...
, social science
Social sciences
Social science is the field of study concerned with society. "Social science" is commonly used as an umbrella term to refer to a plurality of fields outside of the natural sciences usually exclusive of the administrative or managerial sciences...
and music
Music
Music is an art form whose medium is sound and silence. Its common elements are pitch , rhythm , dynamics, and the sonic qualities of timbre and texture...
.
Some of the services for the use in Taverna workflows can be discovered through the BioCatalogue
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....
- a public, centralised and curated registry of Life Science Web services. Taverna workflows can also be shared with other people through the myExperiment
MyExperiment
myExperiment is a social web site for researchers sharing Research Objects such as Scientific Workflows. The Website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as...
social web
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 interactions form the basis of much online activity...
site for scientists. BioCatalogue and myExperiment are another two product from the myGrid
MyGrid
The myGrid consortium is a multi-institutional, multi-disciplinary internationally leading research group focussing on the challenges of eScience...
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, BioMobyBioMOBY
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.- The BioMOBY project :...
and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on remote machines (via ssh
Secure Shell
Secure Shell is a network protocol for secure data communication, remote shell services or command execution and other secure network services between two networked computers that it connects via a secure channel over an insecure network: a server and a client...
), do XPath
XPath
XPath is a language for selecting nodes from an XML document. In addition, XPath may be used to compute values from the content of an XML document...
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. The provenance system for Taverna 2.1 is being co-ordinated with the Open Provenance Model.
Taverna includes the ability to search for services described in BioCatalogue
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....
to include within workflows. However, services do not need to be described within BioCatalogue to be included in workflows.
Taverna also includes the capability to search for workflows on myExperiment
MyExperiment
myExperiment is a social web site for researchers sharing Research Objects such as Scientific Workflows. The Website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as...
. You can download, modify and run the workflows discovered on myExperiment from within the Taverna Workbench. You can also upload you workflows from the Workbench to myExperiment in order to share them with others.
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
Taverna 2 (the second generation of the Taverna software) allows pipelining and streaming of data. This means that services downstream a workflow can start as soon as the first piece of data is received, without waiting for the whole piece of data to become available. It also has improved memory usage allowing the handling of much larger data sets.
Extensibility
Taverna allows developers to plugin new functionality and also to use Taverna within their own products. Taverna has been extended to allow additional components within workflows, for example those from the Chemistry Development KitChemistry Development Kit
The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
, SADI semantic Web services, and caGrid
CaGrid
The cancer Biomedical Informatics Grid, or caBIG is an initiative of the National Cancer Institute, part of the National Institutes of Health. The caGrid computer network and software support caBIG....
. It has also been bundled with other products, for example the Taverna-LC plugin for OpenOffice Calc allows calling services as spreadsheet functions.
Various projects and institutions have run Taverna workflows on grids or have used Taverna to access services on grids, such as KnowARC, NGS (National Grid Service
National Grid Service
The National Grid Service , now entering its seventh year, aims to help UK academics and researchers carry out their research by providing easy to use access to computational, data and other resources...
), EGEE (Enabling Grids for E-sciencE) and caGrid
CaGrid
The cancer Biomedical Informatics Grid, or caBIG is an initiative of the National Cancer Institute, part of the National Institutes of Health. The caGrid computer network and software support caBIG....
.
External tools can be included within Taverna workflows either scripts such as Java Beanshell, though the use of an API Consumer service that generates services for the methods exposed by the tool written in Java or via external tools plugin, which allows users to run tools on a grid or remote/local machine using grid or ssh authentication.
See also
- Bioinformatics workflow management systemsBioinformatics workflow management systemsA bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a specific domain of science, bioinformatics....
- BioCatalogueBioCatalogueThe 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....
- myExperimentMyExperimentmyExperiment is a social web site for researchers sharing Research Objects such as Scientific Workflows. The Website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as...
- WorkflowWorkflowA workflow consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. Workflow may be seen as any abstraction of real work...
- Kepler scientific workflow systemKepler scientific workflow systemKepler is a free software system for designing, executing, reusing, evolving, archiving, and sharing scientific workflows.Kepler's facilities provide process and data monitoring, provenance information, and high-speed data movement solutions...
- Discovery NetDiscovery NetDiscovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services standards....
workflow system - UGENE Workflow Designer
Further reading
Example peer reviewed publications on TavernaExternal links
- Official Taverna Web site
- http://www.myexperiment.orgmyExperiment social webSocial WebThe 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 interactions form the basis of much online activity...
site] for finding and sharing workflows, with special support for Taverna workflows - BioCatalogue - public curated catalogue of Life Science Web services
- Chemistry Development Kit (CDK) Extension for Taverna for Chemoinformatics