Taverna Workbench
Summary
Taverna allows a researcher to construct highly complex analyses over public and private data and computational resources. In effect, this means that experiments can be run in silico.
Taverna runs on a standard computer and is easy to use even if you have a limited background in computing, limited technical resources and support. Taverna currently interacts with over 3000 Web Services. Additional myGrid components, available as Taverna plugins, provide the further abilities such as provenance capture and display and service discovery.
Taverna 2 is a redesign of the Taverna Workbench from the ground up. It has a greater emphasis on scalability to enable the manipulation of larger and more diverse data. The new enactor is more robust with a range of new design features and improvements, including a reduced memory footprint and new data streaming functionality to greatly improve speed and efficiency.
Download
Download the latest version of Taverna (version 2.1)
The older version, Taverna (1.7.2), is also available from this site.
Status
Version 2.1 is the latest release Taverna.
System Requirements
Taverna will run on any modern PC or Mac, running any recent version of Windows, Linux, OS X and most UNIX-like operating systems. A network connection and Java version 5 are required.
Further information
- Homepage
- Documentation for Taverna 2.1
- Documentation for Taverna 1.7
- Licence: Lesser General Public Licence, version 2.1
- Source code can be accessed through the myGrid source-code page
- Mailing lists
- Support can be found on the Support page
Developers
Taverna was developed by the myGrid team based at the University of Manchester.
Taverna 2.0 overview video
- The An overview of Taverna 2 - including writing a workflow
video provides an overview of the new Taverna 2.0 software.
- A bioinformatics video showing the successful application of Taverna for Trypanosomiasis research, and the sharing of workflows on myExperiment, has been produced by the eIUS project. The video can be found on YouTube and on the myGrid website.
myExperiment
myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.
The JISC have produced a series of videos, one of which provides an overview of myExperiment and its benefits to scientists.
Taverna 2.0 tutorials
Taverna platform tutorial
The taverna platform tutorial can be found on the myGrid website
The Taverna platform is a set of APIs and technologies that simplify the process of integrating Taverna and other applications. The Taverna core code makes use of facilities provided by the Java language such as reflection and custom class loading. The platform insulates developers from these parts of Java and allows you to use the Taverna APIs just the same as you’d use any other library. To do this it also handles the initialization and configuration of the various components, such as the workflow enactor, provid
The platform manual and exercises from a developers’ workshop held by Tom Oinn are available online.
The virtual machine used at the workshop is available as a torrent. The password to the virtual machine is password. In order to use the virtual machine you will need the appropriate VMWare - VM Player for Windows or Linux and Fusion for Macs.
BioMoby tutorial
Download a Powerpoint tutorial on how to use Taverna 2 with the emphasis on BioMoby services.
Taverna 1.7 tutorials
Tutorials for Taverna 1.7 can be found on the myGrid tutorial page.
What can it do?
If you are performing multi-step and/or repetitive analyses, or you are copying/pasting results between web pages, and would like to automate the process, then Taverna could be suitable for you.
The following example is based in the field of bioinformatics. However, Taverna is as well-suited to any field of research.
Research into Williams–Beuren Syndrome (WBS), a rare genetic disorder, required the use of multiple services at multiple sites: BLAST for similarity searches, GenBank to retrieve new sequence data and RepeatMasker to mask repetitive DNA sequence regions, GenScan to find gene sequences, and signalP and pscan for functional motif identification tools.
The WBS analyses required time-consuming and repetitive tasks to be performed (intensive input, cut and pasting of results, etc.) which made the analysis mundance and prone to human error.
Automating the WBS analyses with workflows dramatically improved analysis time and the quality of the results. Performing a single WBS analysis manually used to take about one to two weeks, whereas performing the same analysis using Taverna reduced the analysis to a matter of hours.
Projects/companies using Taverna
The following list are just some of the many companiess that have use Taverna.
- BioTeam
- KooPrime
- Lexicon Genetics
- Parquesoft Colombia (non-profit organization)
- PlexLogic
- Unilever
The following list are just some of the many projects that have use Taverna.
- AstroGrid
- Coordination And Sustainability of International Mouse Informatics Resources (CASIMIR)
- Chemistry Development Kit (CDK)
- Developmental Gene Expression Map
- electronic Cultural Heritage made Accessible for Sustainable Exploitation (eChase)
- eFamily
- Enabling Grids for e-SciencE (EGEE)
- ENFIN Project
- GOLD Project
- myIB as part of Integrative Biology
- myTea
- european PLAnt genome database NETwork (PLANET)
- Qurator
- SAMPO Project
- SIMDAT
- User-friendly Tools for Operating Informatics Applications (UTOPIA)
How does it work?
Taverna Workbench allows users to construct complex analysis-workflows from components located on both remote and local machines, run these workflows on their own data and visualise the results.
Working with workflows improves efficiency, accelerates analysis design, reduces the need for ‘house-keeping’ tasks and makes the most of the hardware that’s available to you. A workflow is used to define a complex process from simple building blocks. It represents a set of components and the relations that exist between them. Relations may be in the form of data links, which transfer information from the output of one component to the input of another, or control links, which state some conditions on the execution of a component (e.g. ‘do not run component A until component B has completed’). In Taverna a workflow is realized by an instance of the workflow data model, this appears on disk or on the web as an XML file in the XScufl format.
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List of attachments
| Kind | Attachment Name | Size | Version | Date Modified | Author | Change note |
|---|---|---|---|---|---|---|
swf |
Taverna.swf | 3130.2 kB | 1 | 17-Mar-2009 15:55 | SimonHettrick |
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