Taverna

Taverna: a tool for the composition and enactment of bioinformatics workflows. Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net


References in zbMATH (referenced in 44 articles )

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  1. Andres Veidenberg, Ari L: Pline: automatic generation of modern web interfaces for command-line programs (2020) arXiv
  2. Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow (2019) arXiv
  3. Brandt, Jörgen; Reisig, Wolfgang; Leser, Ulf: Computation semantics of the functional scientific workflow language Cuneiform (2017)
  4. Coelho, L.P.: Jug: Software for Parallel Reproducible Computation in Python (2017) not zbMATH
  5. Posch, S.; Moeller, B.: Alida - Advanced Library for Integrated Development of Data Analysis Applications (2017) not zbMATH
  6. Berk Ekmekci, Charles E. McAnany, Cameron Mura: An Introduction to Programming for Bioscientists: A Python-based Primer (2016) arXiv
  7. Wang, Hai H.; Gibbins, Nick; Payne, Terry R.; Redavid, Domenico: A formal model of the Semantic Web Service Ontology (WSMO) (2012) ioport
  8. Mora, Beatriz; García, Félix; Ruiz, Francisco; Piattini, Mario: Graphical versus textual software measurement modelling: an empirical study (2011) ioport
  9. Wang, Chenqi; Cafferkey, Neil; Kennedy, James; Morrison, John P.: CG3DR: coordination of icosahedral virus reconstruction using condensed graphs (2011) ioport
  10. Wu, Qishi; Gu, Yi: Modeling and simulation of distributed computing workflows in heterogeneous network environments (2011) ioport
  11. Yuan, Dong; Yang, Yun; Liu, Xiao; Chen, Jinjun: On-demand minimum cost benchmarking for intermediate dataset storage in scientific cloud workflow systems (2011)
  12. Callaghan, Scott; Deelman, Ewa; Gunter, Dan; Juve, Gideon; Maechling, Philip; Brooks, Christopher; Vahi, Karan; Milner, Kevin; Graves, Robert; Field, Edward; Okaya, David; Jordan, Thomas: Scaling up workflow-based applications (2010) ioport
  13. Camarasu-Pop, Sorina; Glatard, Tristan; Mościcki, Jakub T.; Benoit-Cattin, Hugues; Sarrut, David: Dynamic partitioning of GATE Monte-Carlo simulations on EGEE (2010) ioport
  14. Coghlan, Brian; Walsh, John; Childs, Stephen; Quigley, Geoff; O’Callaghan, David; Pierantoni, Gabriele; Ryan, John; Simon, Neil; Rochford, Keith: The back-end of a two-layer model for a federated national datastore for Academic research VOs that integrates EGEE data management (2010) ioport
  15. Kumar, Vijay S.; Kurc, Tahsin; Ratnakar, Varun; Kim, Jihie; Mehta, Gaurang; Vahi, Karan; Nelson, Yoonju Lee; Sadayappan, P.; Deelman, Ewa; Gil, Yolanda: Parameterized specification, configuration and execution of data-intensive scientific workflows (2010) ioport
  16. Ma, Jiangang; Cao, Jinli; Zhang, Yanchun: Efficiently supporting secure and reliable collaboration in scientific workflows (2010) ioport
  17. Sroka, Jacek; Hidders, Jan; Missier, Paolo; Goble, Carole: A formal semantics for the Taverna 2 workflow model (2010)
  18. Wu, Yongwei; Yuan, Yulai; Yang, Guangwen; Zheng, Weimin: An adaptive task-level fault-tolerant approach to grid (2010) ioport
  19. Barker, Adam; Weissman, Jon B.; van Hemert, Jano I.: The Circulate architecture: avoiding workflow bottlenecks caused by centralised orchestration (2009) ioport
  20. Corradi, Luca; Mirisola, Valentina; Porro, Ivan; Torterolo, Livia; Fato, Marco; 0001, Paolo Romano; Pfeffer, Ulrich: Survival online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data (2009) ioport

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