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 25 articles )

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  1. Wang, Hai H.; Gibbins, Nick; Payne, Terry R.; Redavid, Domenico: A formal model of the Semantic Web Service Ontology (WSMO) (2012) ioport
  2. Wang, Chenqi; Cafferkey, Neil; Kennedy, James; Morrison, John P.: CG3DR: coordination of icosahedral virus reconstruction using condensed graphs (2011) ioport
  3. Yuan, Dong; Yang, Yun; Liu, Xiao; Chen, Jinjun: On-demand minimum cost benchmarking for intermediate dataset storage in scientific cloud workflow systems (2011)
  4. Camarasu-Pop, Sorina; Glatard, Tristan; Mościcki, Jakub T.; Benoit-Cattin, Hugues; Sarrut, David: Dynamic partitioning of GATE Monte-Carlo simulations on EGEE (2010) ioport
  5. 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
  6. 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
  7. Ma, Jiangang; Cao, Jinli; Zhang, Yanchun: Efficiently supporting secure and reliable collaboration in scientific workflows (2010) ioport
  8. Sroka, Jacek; Hidders, Jan; Missier, Paolo; Goble, Carole: A formal semantics for the Taverna 2 workflow model (2010)
  9. Wu, Yongwei; Yuan, Yulai; Yang, Guangwen; Zheng, Weimin: An adaptive task-level fault-tolerant approach to grid (2010) ioport
  10. Barker, Adam; Weissman, Jon B.; van Hemert, Jano I.: The Circulate architecture: avoiding workflow bottlenecks caused by centralised orchestration (2009) ioport
  11. Kanaris, Ioannis; Mylonakis, Vasileios; Chatziioannou, Aristotelis; Maglogiannis, Ilias; Soldatos, John: HECTOR: enabling microarray experiments over the Hellenic grid infrastructure (2009) ioport
  12. Kiss, Tamas; Kukla, Tamas: Achieving interoperation of grid data resources via workflow level integration (2009) ioport
  13. Neophytou, Panayiotis; Chrysanthis, Panos K.; Labrinidis, Alexandros: Towards continuous workflow enactment systems (2009)
  14. Rendon, Gloria; Ger, Mao-Feng; Kantorovitz, Ruth; Natarajan, Shreedhar; Tilson, Jeffrey; Jakobsson, Eric: Understanding the “horizontal dimension” of molecular evolution to annotate, classify, and discover proteins with functional domains (2009) ioport
  15. Sroka, Jacek; Hidders, Jan: Towards a formal semantics for the process model of the Taverna workbench. I (2009)
  16. Hidders, Jan; Kwasnikowska, Natalia; Sroka, Jacek; Tyszkiewicz, Jerzy; Van den Bussche, Jan: DFL: A dataflow language based on Petri nets and nested relational calculus (2008) ioport
  17. Montagnat, Johan; Glatard, Tristan; Campos Plasencia, Isabel; Castejón, Francisco; Pennec, Xavier; Taffoni, Giuliano; Voznesensky, Vladimir; Vuerli, Claudio: Workflow-based data parallel applications on the EGEE production grid infrastructure (2008) ioport
  18. Hunter, Jane; Cheung, Kwok: Provenance explorer-a graphical interface for constructing scientific publication packages from provenance trails (2007) ioport
  19. Shimosaka, Hisashi; Hiroyasu, Tomoyuki; Miki, Mitsunori: Distributed workflow management system based on publish-subscribe notification for Web services (2007) ioport
  20. Tiwari, Abhishek; Sekhar, Arvind K.T.: Workflow based framework for life science informatics (2007)

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