The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

Wolstencroft, Katy; Haines, Robert; Fellows, Donal; Williams, Alan; Withers, David; Owen, Stuart; Soiland‐Reyes, Stian; Dunlop, Ian; Nenadić, Aleksandra; Fisher, Paul; Bhagat, Jiten; Belhajjame, Khalid; Bacall, Finn; Hardisty, Alex; Hidalga, Abraham Nieva de la; Vargas, Maria P. Balcazar; Sufi, Shoaib; Goble, Carole

doi:10.1093/nar/gkt328

Cited by 624 publications

(465 citation statements)

References 21 publications

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“…Rserve is currently being used by several mature projects, among them the Taverna workflow management system 5 .…”

Section: Methodsmentioning

confidence: 99%

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Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Gonçalvès

Sáez-Rodríguez

2013

F1000Res

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There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape plug-in termed Cyrface that allows Cytoscape plug-ins to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it links the R packages with the capabilities of Cytoscape and its plug-ins, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/).

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“…Rserve is currently being used by several mature projects, among them the Taverna workflow management system 5 .…”

Section: Methodsmentioning

confidence: 99%

“…Workflow management systems such as Taverna 5 and Galaxy 6– 8 can call R packages from a graphical user interface (GUI)-based interface. Taverna is a standalone Java open-source tool for the general development and execution of workflows.…”

Section: Introductionmentioning

confidence: 99%

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Gonçalvès

Sáez-Rodríguez

2013

F1000Res

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“…Common use cases are parameter convergence, restarts in molecular dynamics simulations, multi-scale simulations, data-mining analysis, and other situations when results of calculations with one code are used as inputs for different codes. In such cases, it is beneficial to have a system that encodes the workflow and manages its execution [48,49,50,51,52].…”

Section: Scientific Workflowsmentioning

confidence: 99%

AiiDA: automated interactive infrastructure and database for computational science

Pizzi

Cepellotti

Sabatini

et al. 2016

Computational Materials Science

507

417

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Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from computer science to manage, preserve, and share these computational efforts. We illustrate here our paradigm sustaining such vision, based around the four pillars of Automation, Data, Environment, and Sharing. We then discuss its implementation in the open-source AiiDA platform (http://www.aiida.net), that has been tuned first to the demands of computational materials science. AiiDA's design is based on directed acyclic graphs to track the provenance of data and calculations, and ensure preservation and searchability. Remote computational resources are managed transparently, and automation is coupled with data storage to ensure reproducibility. Last, complex sequences of calculations can be encoded into scientific workflows. We believe that AiiDA's design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows.

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“…A Taverna 19 workflow was used to search all data against genomederived sequences and combine the results into a spectral library (Figure 3). Mass spectrometry data from both the indepth analysis (SDS-PAGE fractionation and in-gel digestion) and from samples digested in-solution (already used for the hierarchical clustering) were included in the library.…”

Section: Organ Differentiated Zebrafish Spectral Librarymentioning

confidence: 99%

Identifying Proteins in Zebrafish Embryos Using Spectral Libraries Generated from Dissected Adult Organs and Tissues

et al. 2014

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Spectral libraries provide a sensitive and accurate method for identifying peptides from tandem mass spectra, complementary to searching genome-derived databases or sequencing de novo. Their application requires comprehensive libraries including peptides from low-abundant proteins. Here we describe a method for constructing such libraries using biological differentiation to "fractionate" the proteome by harvesting adult organs and tissues and build comprehensive libraries for identifying proteins in zebrafish (Danio rerio) embryos and larvae (an important and widely used model system). Hierarchical clustering using direct comparison of spectra was used to prioritize organ selection. The resulting and publicly available library covers 14 164 proteins, significantly improved the number of peptide-spectrum matches in zebrafish developmental stages, and can be used on data from different instruments and laboratories. The library contains information on tissue and organ expression of these proteins and is also applicable for adult experiments. The approach itself is not limited to zebrafish but would work for any model system.

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The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

Cited by 624 publications

References 21 publications

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

AiiDA: automated interactive infrastructure and database for computational science

Identifying Proteins in Zebrafish Embryos Using Spectral Libraries Generated from Dissected Adult Organs and Tissues

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