Meta-workflows: pattern-based interoperability between Galaxy and Taverna

@inproceedings{Abouelhoda2010MetaworkflowsPI,
  title={Meta-workflows: pattern-based interoperability between Galaxy and Taverna},
  author={Mohamed Ibrahim Abouelhoda and Shady Alaa and Moustafa M. Ghanem},
  booktitle={Wands '10},
  year={2010}
}
Taverna and Galaxy are two workflow systems developed specifically for bioinformatics applications. For sequence analysis applications, some tasks can be implemented easily on one system but would be difficult, or infeasible, to be implemented on the other. One solution to overcome this situation is to combine both tools in a unified framework that seamlessly makes use of the best features of each tool. In this paper, we present the architecture and implementation of a high-level system that… 

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References

SHOWING 1-10 OF 26 REFERENCES
Taverna: a tool for building and running workflows of services
TLDR
Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services, to perform a range of different analyses, such as sequence analysis and genome annotation.
Taverna: a tool for the composition and enactment of bioinformatics workflows
TLDR
The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community that is written in a new language called Scufl, where by each step within a workflow represents one atomic task.
The Triana Workflow Environment: Architecture and Applications
TLDR
In this chapter, the Triana workflow environment is described and an overview of Taverna, a system designed to support scientists using Grid technology to conduct in silico experiments in biology is given.
Scientific workflow systems - can one size fit all?
  • V. CurcinM. Ghanem
  • Computer Science
    2008 Cairo International Biomedical Engineering Conference
  • 2008
TLDR
This paper provides a high-level framework for comparing the systems based on their control flow and data flow properties with a view of both informing future research in the area by academic researchers and facilitating the selection of the most appropriate system for a specific application task by practitioners.
The discovery net system for high throughput bioinformatics
TLDR
This work built a Grid based application for Genome Annotation that includes workflows for automatic nucleotide annotation, annotation of predicted proteins and text analysis based on metabolic profiles and textAnalysis.
Workflow Interoperability in Grid-based Systems
TLDR
The main requirements for developing and using cross-origination grid-based workflows for engineering applications and product design are discussed and some of the higher-level issues and problems that exist when multiple workflow systems exist within the same environment are described.
Scientific workflow management and the Kepler system
TLDR
Characteristics of and requirements for scientific workflows as identified in a number of application projects are described, and some key features of Kepler and its underlying Ptolemy II system, planned extensions, and areas of future research are described.
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.
Visual Grid Workflow in Triana
TLDR
This approach, which the authors refer to as the Visual GAT, differs substantially from other approaches because it base its implementation on application level requirements and model such primitives from a user's perspective by hiding as much complexity as possible without undermining the core capabilities required.
Galaxy: a platform for interactive large-scale genome analysis.
TLDR
An interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results.
...
...