Taverna: lessons in creating a workflow environment for the life sciences

@article{Oinn2006TavernaLI,
  title={Taverna: lessons in creating a workflow environment for the life sciences},
  author={T. Oinn and R. Greenwood and M. Addis and M. Alpdemir and Justin Ferris and Kevin Glover and C. Goble and Antoon Goderis and D. Hull and D. Marvin and Peter Li and P. Lord and Matthew R. Pocock and M. Senger and R. Stevens and A. Wipat and C. Wroe},
  journal={Concurrency and Computation: Practice and Experience},
  year={2006},
  volume={18}
}
Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co‐ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information… Expand
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References

SHOWING 1-10 OF 77 REFERENCES
Contextualised Workflow Execution in MyGrid
TLDR
The benefits that derive from the provision of integrated access to contextual information that links the phases of a problem-solving activity are illustrated, so that the steps of a solution do not happen in isolation, but rather as the components of a coherent whole. Expand
Experiences with e-Science workflow specification and enactment in bioinformatics
TLDR
The EPSRC funded Grid project has developed a graphical toolset and workflow enactor which uses its own high level representation of a process flow, including specification of processing units, data transfers and execution constraints. Expand
An Ontology-Driven Framework for Data Transformation in Scientific Workflows
TLDR
This paper defines a generic framework for transforming heterogeneous data within scientific workflows, which relies on a formalized ontology, which serves as a simple, unstructured global schema. Expand
Performing in silico Experiments on the Grid : A Users Perspective
e-Science and the Grid are not the same; the large-scale movement of data and the exploitation of computation is not the same as the creation, performance and management of an in silico experiment.… Expand
Using Semantic Web Technologies for Representing E-science Provenance
TLDR
This work explores the use of Semantic Web technologies such as RDF, and ontologies to support its representation and used existing initiatives such as Jena and LSID, to generate and store such material. Expand
Performing \emph{In Silico} Experiments on the Grid: A Users' Perspective
TLDR
The Grid project is introduced and the nature of an in silico experiment for the bioinformatics domain is explored, and the general user requirements for an empirical e-Scientist are reviewed. Expand
A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework
TLDR
PathPort, short for Pathogen Portal, employs a generic, web-services based framework to deal with some of the problems identified by the bioinformatics community, using two major components. Expand
Knowledge Integration
TLDR
My Grid's second category of services supports the scientific method and best practice found at the bench but often neglected at the workstation, specifically provenance management, change notification, and personalization. Expand
A Knowledge-Based Approach to Interactive Workflow Composition
Complex applications in many areas, including scientific computations and business-related web services, are created from collections of components to form computational workflows. In many cases end… Expand
Workflow Patterns
TLDR
A number of workflow patterns addressing what the authors believe identify comprehensive workflow functionality are described, providing the basis for an in-depth comparison of a number of commercially availablework flow management systems. Expand
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