Taverna: a tool for building and running workflows of services

By Duncan Hull, K. Wolstencroft, Robert Stevens, Carole A. Goble, Matthew R. Pocock, Peter Li, T. Oinn. Nucleic Acids Res., 2006

1,092 citations recorded by the source corpus.

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from .

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/67e012b7d5feefc34f45c9c50bde5035e7cd8c74

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Citations in the corpus

The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, background): “It also supports many third party packages such as Taverna (2), Galaxy (3), Cytoscape (4) and biomaRt (5), which part of the Bioconductor (6) library.”
The Arabidopsis Information Resource (TAIR): gene structure and function annotation (2007, background): “net/) (4) or aggregator pages such as tAIGa (http://mips.”
Characterization of scientific workflows (2008, methodology): “It also allows users to launch their workflows from the website using the Taverna [21] workbench.”
Dynamic QoS Management and Optimization in Service-Based Systems (2011, methodology): “Taverna is widely used in the development of scientific workflows in application domains, including bioinformatics, chemoinformatics, astronomy, and social sciences.”
The iPlant Collaborative: Cyberinfrastructure for Plant Biology (2011, methodology): “…APIs is exposed via HTTP, and can be used by web applications like the DE, workflow management applications such as Taverna (Oinn et al., 2004; Hull et al., 2006; Kawas et al., 2006; Krabbenhoft et al., 2008; Lanzen and Oinn, 2008; Li et al., 2008; Wassink et al., 2009; Kano et al., 2010),…”
Structuring and extracting knowledge for the support of hypothesis generation in molecular biology (2009, neutral): “In this context, it will be interesting to see if we will be able to replace our workflow model and link directly to the light weight provenance model that is being implemented for Taverna 2 [41].”
myExperiment: a repository and social network for the sharing of bioinformatics workflows (2010, methodology): “This has been used by the myExperiment plug-in for Taverna that allows its workbench to access and download workflows directly from myExperiment (20), integration with BioCatalogue and the development of Facebook applications and Google Gadgets.”
BioMart – biological queries made easy (2009, methodology): “The Taverna workbench [7,26], another open source software package which integrates BioMart, allows interoperation between local and remote analysis tools and databases by providing an environment for the design and execution of workflow experiments.”
PubChem3D: a new resource for scientists (2011, neutral): “, Taverna [44], Pipeline Pilot [45]).”
An introduction to Docker for reproducible research (2014, background): “Two dominant paradigms have emerged to address these issues so far: workflow software [1, 13] and virtual machines [5, 12].”
ArrayExpress—a public database of microarray experiments and gene expression profiles (2006, positive): “All of Expression Proﬁler’s components can be accessed using SOAP-based web services and can be incorporated into bioinformatics workﬂows using Taverna (8).”
A survey of tools for variant analysis of next-generation genome sequencing data (2013, methodology): “The ‘Taverna’ [144] workflow management system stores workflows in a format that is simple 272 Pabinger et al.”
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows (2013, methodology): “The server provides programmatic access to services of multiple DIANA algorithms and a complete integration with the Taverna Workflow Management System (WMS) (10), using the in-house developed DIANA-Taverna Plug-in.”
RSAT: regulatory sequence analysis tools (2008, methodology): “In addition, workflows can be designed without any programming, using the graphical user interface of the program Taverna (18,19).”