Evolution of grid-based services for Diffusion Tensor Image analysis

Caan, Matthan W.A.; Shahand, Shayan; Vos, Frans M.; Kampen, Antoine H. C. van; Olabarriaga, Sílvia D.

doi:10.1016/j.future.2012.03.007

Cited by 4 publications

(2 citation statements)

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“…With the e-BioInfra, the development and execution of workflows for high-throughput computing became straightforward, and the platform became heavily used at the AMC for medical imaging [2] and DNA sequencing [3] data analyses 1 . This translates into more than 40 different workflows for data analysis so far, of which many more versions exist.…”

Section: The Amc E-bioinfra Experiencementioning

confidence: 99%

“…At the Academic Medical Center of the University of Amsterdam (AMC), a workflow-based software platform has been adopted for four years now to enable medical imaging [2] and DNA sequencing [3] research. Workflows are extensively used as the primary abstraction for programming and running applications on the Dutch production grid infrastructure, facilitating access to both advanced and novice users.…”

Section: Introductionmentioning

confidence: 99%

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Exploring Dynamic Enactment of Scientific Workflows Using Pilot-Abstractions

Santcroos

Schaik

Shahand

et al. 2013

2013 13th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing

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Current workflow abstractions in general lack: (a) an adequate approach to handle distributed data and (b) proper separation between logical tasks and data-flow from their mapping onto physical locations. As the complexity and dynamism of data and processing distribution have increased, optimized mapping of logical tasks to physical resources have become a necessity to avoid bottlenecks. We argue that the management of dynamic data and compute should become part of the runtime system of workflow engines to enable workflows to scale as necessary to address big data challenges and fully exploit distributed computing infrastructures (DCI). In this paper we explore how the P* model for pilot-abstractions, which proposes a clear separation between the logical compute and data units and their realization as a job or a file in some physical resource, could provide these capabilities for such a runtime environment. The Pilot-API provides a general-purpose interface to pilotabstractions and the ability to assign compute and data resources to them. We share our experience of using the case study of a DNA sequencing pipeline, to re-implement the workflow using the Pilot-API. This first exercise, which resulted in a running application that is discussed here, illustrates the potential of this API to address (a) and (b). Our initial results indicate that the pilot abstractions (as captured by the P* model) offer an interesting approach to explore the design of a new generation of workflow management systems and runtime environments that are capable of intelligently deciding on application-aware late binding to physical resources.

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Section: The Amc E-bioinfra Experiencementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%