Skip to main content

Using the Grid for the Interactive Workflow Management in Biomedicine

  • Conference paper
Book cover Grid Enabled Remote Instrumentation

Part of the book series: Signals and Communication Technology ((SCT))

  • 616 Accesses

Abstract

According to the virtual physiological human paradigm, integration is often\break required among different levels and disciplines. Large, distributed and heterogeneous repositories, as well as computationally demanding analysis tools, are more and more involved in biomedical studies. Both for storage of distributed biomedical data and metadata and for access to distributed analysis tools, a Grid-based approach may provide a shared, standardized and reliable solution. To make users able to easily access available services and data, a Grid portal has been implemented in order to hide the complexity of the framework. The portal is intended to act as Grid services provider and as Web interface for managing workflow enactment and management on the Grid. Workflows may be submitted as Grid jobs through a service-based workflow engine and monitored during execution. As a first case study for testing workflow functionalities of the Grid portal, an application is presented for the search and analysis of microarray data.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alfieri R, Barbera R, Belluomo P, Cavalli A, Cecchini R, Chierici A, Fiaschini V, Dell’Agnello L, Donno F, Ferro E. “The INFN-Grid testbed”, Future Gen. Comput. Syst. 2005, 21(2)249–258.

    Article  Google Scholar 

  2. Andronico A, Barbera R, Falzone A, Kunszt P, Re GL, Pulvirenti A, Rodolico A. “Genius: a simple and easy way to access computational and data grids”, Future Gen. Comput. Syst. 2003, 19(6)805–813.

    Article  Google Scholar 

  3. Gil Y, Deelman E, Blythe J, Kessleman C, Tangmunarunkit H, “Artificial intelligence and grids: workflow planning and beyond”, IEEE Intell. Syst. special issue on e-science 2004, 19(1)26–33.

    Article  Google Scholar 

  4. Glatard T, Montagnat J, Pennac X. “MOTEUR grid-enabled data-intensive workflowmanager”, Proc. Healthgrid 2006, Valencia, Spain, June 7–9, 2006.

    Google Scholar 

  5. Li C, Wong WH. “Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection”, Proc. Natl.Acad. Sci. USA 2001, 98:31–36.

    Article  Google Scholar 

  6. Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z. “MARS: microarray analysis, retrieval, and storage system”, BMC Bioinform. 2005, 6(1): 101.

    Article  Google Scholar 

  7. Muggleton SH. “2020 computing: exceeding human limits” Commentary, Nature,22 March 2006, 440: 409–410.

    Google Scholar 

  8. Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedrén S, Bergh J. “Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts”, Breast Cancer Res. 2005, 7(6): R953–64.

    Article  Google Scholar 

  9. Porro I, Torterolo L, Corradi L, Fato M, Papadimitropoulos A, Scaglione S, Schenone A, Viti F. “A Grid based solution for management and analysis of microarrays in distributed experiments” BMC Bioinform. (accepted).

    Google Scholar 

  10. Romano P, Bertolini G, De Paoli F, Fattore M, Marra D, Mauri G, Merelli E, Porro I, Scaglione S, Milanesi L. “Oncology over Internet: integrating data and analysis of oncology interest on the net by means of workflows”, International Workshop on Integrative Bioinformatics Complex Metabolic Networks, Bielefeld, Germany, July 4–5, 2005.

    Google Scholar 

  11. N. Santos and B. Koblitz, “Metadata services on the grid”, in Proc. of Advanced Computing and Analysis Techniques (ACAT’05), Zeuthen, Berlin, May 2005.

    Google Scholar 

  12. Stratowa C. “XPS, a novel framework for distributed storage and analysis of microarray data in the terabyte range: an alternative to bioConductor”, Proceedings of the 3rd International Workshop on Distributed Statistical Computing, 2003.

    Google Scholar 

  13. Thorsten F. “ODD genes – from microarray data to discovery, using the Grid and high performance computing”, Scottish Center for Genomics Technology and Informatics (SC-GTI) 3rd E-BioSci/ORIEL Annual Workshop, Hinxton Hall Conference Centre, Hinxton, England, October 12–15, 2004, www.gti.ed.ac.uk.

    Google Scholar 

  14. Tuecke S, Welch V, Engert D, Pearlman L, Thompson M. “Internet X.509 public key infrastructure (PKI) proxy certificate profile”, IETF RFC 3820, June 2004.

    Google Scholar 

  15. “Towards Virtual Physiological Human: multilevel modelling and simulation of the human anatomy and physiology – White Paper”, edited by European Commission – DG INFSO & DG JRC, Bruxelles, December 2005.

    Google Scholar 

  16. http://www.enginframe.com.

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this paper

Cite this paper

Porro, I., Torterolo, L., Fato, M., Schenone, A., Melato, M. (2009). Using the Grid for the Interactive Workflow Management in Biomedicine. In: Davoli, F., Meyer, N., Pugliese, R., Zappatore, S. (eds) Grid Enabled Remote Instrumentation. Signals and Communication Technology. Springer, New York, NY. https://doi.org/10.1007/978-0-387-09663-6_39

Download citation

  • DOI: https://doi.org/10.1007/978-0-387-09663-6_39

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-0-387-09662-9

  • Online ISBN: 978-0-387-09663-6

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics