Taverna: a tool for the composition and enactment of bioinformatics workflows

By T. Oinn, M. Addis, Justin Ferris, Darren Marvin, M. Senger, Robert Mark Greenwood, T. Carver, Kevin Glover, Matthew R. Pocock, A. Wipat and 1 more. Bioinform., 2004

1,825 citations recorded by the source corpus.

Subfields: Political Science and International Relations, Safety Research, Sociology and Political Science

View Paper: https://www.semanticscholar.org/paper/36789799e464aa7465125ff8e778939843a0e89b

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In Political Science and International Relations

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Citations in the corpus

Predicting protein function from sequence and structural data. (2005, methodology): “In Taverna [65], a workﬂow can be drawn up on screen using drag and drop methods, and then initiated.”
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010, methodology): “Taverna is a workflow system that supports the creation and use of workflows for analyzing genomic data [33].”
Snakemake - a scalable bioinformatics workflow engine (2012, neutral): “Systems such as Biopipe (Hoon et al ., 2003), Taverna (Oinn et al ., 2004), Galaxy (Goecks et al. , 2010), GeneProf (Halbritter et al ., 2011) or PegaSys (Shah et al. , 2004) are easy to learn and use through their graphical user interface.”
A Particle Swarm Optimization-Based Heuristic for Scheduling Workflow Applications in Cloud Computing Environments (2010, methodology): “The Taverna project [12] has developed a tool for the composition and enactment of bioinformatics workflows for the life science community.”
A Survey of Data-Intensive Scientific Workflow Management (2015, methodology): “Several SWfMSs, e.g. Pegasus [41,42], Swift [144], Kepler [10], Taverna [104], Galaxy [60], Chiron [102] and SWfMS gateway frameworks such as WS-PGRADE/gUSE [78] are now used intensively by various research communities, e.g. astronomy, biology, computational engineering.”
Statistical strategies for avoiding false discoveries in metabolomics and related experiments (2007, methodology): “…useful concept in bioinformatics (Goble et al., 2001) is the concept of the pipeline (Potter et al., 2004; Brown et al., 2005) or workflow (Peleg et al., 2002; Oinn et al., 2004, 2006; Stevens et al., 2004; Romano et al., 2005), especially in the present context for the analysis of omics data.”
State of the nation in data integration for bioinformatics (2008, background): “Others, like Taverna [39], have an open type system where the data passed between the workflow steps is ‘‘massaged” into shape by special”
A taxonomy of scientific workflow systems for grid computing (2005, neutral): “Taverna [17] DAG Abstract Concrete User-directed”
STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008, methodology): “To facilitate the integration of STRING into network tools like Cytoscape (27) and workﬂow engines like Taverna (28), we have created an application programming interface (API) that allows access to the interaction network in computer-readable formats (Figure 3).”
Ten Simple Rules for Reproducible Computational Research (2013, background): “Such executable descriptions [10] might come in the form of simple shell scripts or makefiles [15,16] at the command line, or in the form of stored workflows in a workflow management system [10,11,13,17,18].”
A Taxonomy of Workflow Management Systems for Grid Computing (2005, background): “Taverna [95] is the workflow management system of the my Grid [113] project, which aims to exploit Grid technology to develop high-level middleware for supporting personalized in silico experiments in biology.”
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).”