Accelerating medical research using the swift workflow system

Tiberiu Stef-Praun, Benjamin Clifford, Ian Foster, Uri Hasson, Mihael Hategan, Steven L. Small, Michael Wilde, Yong Zhao

Research output: Chapter in Book/Report/Conference proceedingConference contribution

15 Citations (Scopus)

Abstract

Both medical research and clinical practice are starting to involve large quantities of data and to require large-scale computation, as a result of the digitization of many areas of medicine. For example, in brain research-the domain that we consider here-a single research study may require the repeated processing, using computationally demanding and complex applications, of thousands of files corresponding to hundreds of functional MRI studies. Execution efficiency demands the use of parallel or distributed computing, but few medical researchers have the time or expertise to write the necessary parallel programs. The Swift system addresses these concerns. A simple scripting language, SwiftScript, provides for the concise high-level specification of workflows that invoke various application programs on potentially large quantities of data. The Swift engine provides for the efficient execution of these workflows on sequential computers, parallel computers, and/or distributed grids that federate the computing resources of many sites. Last but not least, the Swift provenance catalog keeps track of all actions performed, addressing vital bookkeeping functions that so often cause difficulties in large computations. To illustrate the use of Swift for medical research, we describe its use for the analysis of functional MRI data as part of a research project examining the neurological mechanisms of recovery from aphasia after stroke. We show how SwiftScript is used to encode an application workflow, and present performance results that demonstrate our ability to achieve significant speedups on both a local parallel computing cluster and multiple parallel clusters at distributed sites.

Original languageEnglish (US)
Title of host publicationFrom Genes to Personalized HealthCare
Subtitle of host publicationGrid Solutions for the Life Sciences - Proceedings of HealthGrid 2007
PublisherIOS Press
Pages207-216
Number of pages10
ISBN (Print)9781586037383
StatePublished - Jan 1 2007
Externally publishedYes
Event5th Conference of the HealthGrid Association, HealthGrid 2007 - Geneva, Switzerland
Duration: Apr 24 2007Apr 27 2007

Publication series

NameStudies in Health Technology and Informatics
Volume126
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Conference

Conference5th Conference of the HealthGrid Association, HealthGrid 2007
CountrySwitzerland
CityGeneva
Period4/24/074/27/07

Fingerprint

Workflow
Biomedical Research
Research
Magnetic Resonance Imaging
Parallel processing systems
Aptitude
Aphasia
Language
Stroke
Research Personnel
Medicine
Analog to digital conversion
Efficiency
Distributed computer systems
Application programs
Brain
Engines
Specifications
Recovery
Processing

Keywords

  • Brain research
  • Grid Computing
  • Workflows

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Stef-Praun, T., Clifford, B., Foster, I., Hasson, U., Hategan, M., Small, S. L., ... Zhao, Y. (2007). Accelerating medical research using the swift workflow system. In From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007 (pp. 207-216). (Studies in Health Technology and Informatics; Vol. 126). IOS Press.

Accelerating medical research using the swift workflow system. / Stef-Praun, Tiberiu; Clifford, Benjamin; Foster, Ian; Hasson, Uri; Hategan, Mihael; Small, Steven L.; Wilde, Michael; Zhao, Yong.

From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. IOS Press, 2007. p. 207-216 (Studies in Health Technology and Informatics; Vol. 126).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Stef-Praun, T, Clifford, B, Foster, I, Hasson, U, Hategan, M, Small, SL, Wilde, M & Zhao, Y 2007, Accelerating medical research using the swift workflow system. in From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. Studies in Health Technology and Informatics, vol. 126, IOS Press, pp. 207-216, 5th Conference of the HealthGrid Association, HealthGrid 2007, Geneva, Switzerland, 4/24/07.
Stef-Praun T, Clifford B, Foster I, Hasson U, Hategan M, Small SL et al. Accelerating medical research using the swift workflow system. In From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. IOS Press. 2007. p. 207-216. (Studies in Health Technology and Informatics).
Stef-Praun, Tiberiu ; Clifford, Benjamin ; Foster, Ian ; Hasson, Uri ; Hategan, Mihael ; Small, Steven L. ; Wilde, Michael ; Zhao, Yong. / Accelerating medical research using the swift workflow system. From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007. IOS Press, 2007. pp. 207-216 (Studies in Health Technology and Informatics).
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