Taverna

Category Cross-Omics>Workflow Knowledge Bases/Systems/Tools

Abstract Taverna is an open-source workflow tool which provides a workflow language (scufl - Simple Conceptual Unified Flow Language) and graphical interface to facilitate the easy building, running and editing of workflows over distributed computer resources.

The manufacturer considers a ‘workflow’ (see below...) to mean the specification and execution of ad-hoc ‘in-silico experiments’ using informatics resources.

A workflow-based approach allows the e-Scientist to describe and enact their experimental processes in a structured, repeatable and verifiable way.

Taverna is used as shorthand for two (2) pieces of software:

1) Taverna workbench - allows the creation and editing of workflows that call services;

2) Taverna engine - executes the workflow, either on your own machine or on an external service.

Taverna workbench, by default, includes a ‘Taverna engine’ to allow local enactment of workflows. Remote enactment is achieved by the remote execution plug-in within the workbench calling a Taverna Remote Execution Service.

The ‘Taverna Remote Execution’ plug-in is a plug-in for Taverna that allows workflows to be run on a Remote Execution Server.

‘Taverna Remote Execution’ Service - The Taverna Server combines a Remote Execution Service with the Remote Execution plug-in for Taverna 1.7 to give a lab the possibility to set up a dedicated server for executing workflows remotely.

The user can submit workflows from Taverna 1.7, detach, and check their execution status later either from Taverna or from a web page.

Workflow(s) –

A workflow represents an experimental protocol, or methodology. Each workflow is constructed from one or more services, which may be connected directly into another service.

This enables a chain of services to be linked together in a systematic manner. As a consequence, Workflows enable the automation of in silico experiments (from small to very large-scale) and the formalization of experimental protocols.

Taverna allows researchers to combine and co-ordinate distributed analysis tools and data resources into workflows.

Each service and piece of data can be located on your own machine or anywhere on the internet, to which you have access. The services that you include in your workflows are Not pre-defined, allowing you to customize the workflow to your own needs.

During the construction of a workflow, users can search for services that they require, or select one they already know about (including their own services or scripts).

This is conducted dynamically, meaning that you can add services as and when required.

Once constructed, researchers are then able to execute the workflow from within Taverna, allowing input data to be sent from one service to the next without the need for any user interaction (unless specified otherwise with interaction services).

Note: More than 350 organizations around the world, both academic and commercial, are known to use Taverna.

Taverna Success Stories –

Taverna has been used in a large number of different domains from music to meteorology to medicine.

The success stories shown here represent a very small sample of the impact that Taverna has had on science and scientists.

1) In general workflow use - The recovery of data about mutated proteins; the identification of mismatches and possible annotations in workflows; and

The use of Taverna for ‘knowledge extraction’ workflows.

2) In chemistry - The integration of a chemistry-specific toolkit with the Taverna system.

3) In medicine - The use of imaging algorithms within workflows.

4) In social science - The modeling of the ‘open source’ software community.

5) In disease-related research - The analysis of the Anthrax bacterium; the study of resistance into Trypanosomiasis (sleeping sickness);

The identification of genes linked to Graves disease; and The characterization of genes associated with Williams-Beuren syndrome.

6) In the arts - The composition of music using web-services for synthesis.

7) In education (as well as its use for teaching purposes) - The creation of courses from individual learning activities and resources.

8) In Bioinformatics - The measuring of enzyme characteristics of yeast;

The integration of plant genome resources; the annotation of genomes; and

The examination of ‘gene expression’ from MicroArray data, using R.

Taverna 1.7.1’s features/capabilities include:

1) Create, edit and run workflows –

Compose new workflows; Load existing workflows possibly published by others; View workflow layouts and logic;

Modify existing workflows; Use nested workflows (sub-workflows);

Execute existing workflows; Specify workflow inputs; Publish workflows for use by others;

Implicitly iterate over calls of services; Failover, so that if one service fails another can be called;

Monitor execution; Manage jobs and results;

Visualize the results; and Save and browse execution provenance.

2) Discover and create services –

Include multiple service types - Web Services Description Language (WSDL), BioMart, BioMoby, R, Beanshell, etc;

Create new components (Processors); Edit component interface; Employ script languages;

User interaction as part of the workflow; and Discover services from a registry.

3) Workflow discovery -- Browse, search, run workflows from myExperiment (see G6G Abstract Number 20513).

4) Extend and interact -- Integrate external tools; Extensible / Plug-in management; and Creation of services from Java classes.

5) Non-graphical execution -- Command line access; Remote execution of a workflow on another machine.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site Taverna

Price Contact manufacturer.

G6G Abstract Number 20514

G6G Manufacturer Number 102854