[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ Skip to main content
Springer Nature Link
Log in

A Grid-Enabled Gateway for Biomedical Data Analysis

  • Published:
Journal of Grid Computing Aims and scope Submit manuscript

Abstract

Biomedical researchers can leverage Grid computing technology to address their increasing demands for data- and compute-intensive data analysis. However, usage of existing Grid infrastructures remains difficult for them. The e-infrastructure for biomedical science (e-BioInfra) is a platform with services that shield middleware complexities, in particular workflow management and monitoring. These services can be invoked from a web-based interface, called e-BioInfra Gateway, to perform large scale data analysis experiments, such that the biomedical researchers can focus on their own research problems. The gateway was designed to simplify usage both by biomedical researchers and e-BioInfra administrators, and to support straightforward extensions with new data analysis methods. In this paper we present the architecture and implementation of the gateway, also showing statistics for its usage. We also share lessons learned during the gateway development and operation. The gateway is currently used in several biomedical research projects and in teaching medical students the principles of data analysis.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
£29.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Alfieri, R., Cecchini, R., Ciaschini, V., dell’Agnello, L., Frohner, Á., Gianoli, A., Lõrentey, K., Spataro, F.: Voms, an authorization system for virtual organizations. In: Fernández Rivera, F., Bubak, M., Gómez Tato, A., Doallo, R. (eds.) Grid Computing. Lecture Notes in Computer Science, vol. 2970, pp. 33–40. Springer, Berlin/Heidelberg (2004)

    Chapter  Google Scholar 

  2. Altunay, M., Avery, P., Blackburn, K., Bockelman, B., Ernst, M., Fraser, D., Quick, R., Gardner, R., Goasguen, S., Levshina, T., Livny, M., McGee, J., Olson, D., Pordes, R., Potekhin, M., Rana, A., Roy, A., Sehgal, C., Sfiligoi, I., Wuerthwein, F.: A Science Driven Production Cyberinfrastructure—the Open Science Grid. J. Grid Computing 9, 201–218 (2011)

    Article  Google Scholar 

  3. Andronico, G., Ardizzone, V., Barbera, R., Becker, B., Bruno, R., Calanducci, A., Carvalho, D., Ciuffo, L., Fargetta, M., Giorgio, E., La Rocca, G., Masoni, A., Paganoni, M., Ruggieri, F., Scardaci, D.: e-infrastructures for e-science: a global view. J. Grid Computing 9, 155–184 (2011)

    Article  Google Scholar 

  4. Barbera, R., Andronico, G., Donvito, G., Falzone, A., Keijser, J.J., Rocca, G.L., Milanesi, L., Maggi, G.P., Vicario, S.: A Grid portal with robot certificates for bioinformatics phylogenetic analyses. Concurrency Computat.: Pract. Exper. 23(3), 246–255 (2011)

    Article  Google Scholar 

  5. Berkeley Database Information Index (BDII): https://twiki.cern.ch/twiki/bin/view/EGEE/BDII. Accessed 23 May 2012

  6. Basney, J., Humphrey, M., Welch, V.: The myproxy online credential repository. Softw. Pract. Exper. 35(9), 801–816 (2005)

    Article  Google Scholar 

  7. Bertini, I., Case, D.A., Ferella, L., Giachetti, A., Rosato, A.: A Grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics 27(17), 2384–2390 (2011). doi:10.1093/bioinformatics/btr415

    Article  Google Scholar 

  8. Birkenheuer, G., Blunk, D., Breuers, S., Brinkmann, A., Fles, G., Gesing, S., et al.: MoSGrid: progress of workflow driven chemical simulations. In: Proceedings of Grid Workflow Workshop (GWW) (2011)

  9. Breton, V., Dean, K., Solomonides, T., Blanquer, I., Hernandez, V., Medico, E., Maglaveras, N., Benkner, S., Lonsdale, G., Lloyd, S., Hassan, K., McClatchey, R., Miguet, S., Montagnat, J., Pennec, X., De Neve, W., De Wagter, C., Heeren, G., Maigne, L., Nozaki, K., Taillet, M., Bilofsky, H., Ziegler, R., Hoffman, M., Jones, C., Cannataro, M., Veltri, P., Aloisio, G., Fiore, S., Mirto, M., Chouvarda, I., Koutkias, V., Malousi, A., Lopez, V., Oliveira, I., Sanchez, J.P., Martin-Sanchez, F., De Moor, G., Claerhout, B., Herveg, J.A.: The healthgrid white paper. Stud. Health Technol. Inform. 112, 249–321 (2005)

    Google Scholar 

  10. Caan, M., Shahand, S., Vos, F., van Kampen, A., Olabarriaga, S.: Evolution of Grid-based services for diffusion tensor image analysis. Future Gener. Comput. Syst. 28(8), 1194–1204 (2012)

    Article  Google Scholar 

  11. Caan, M., Vos, F., van Kampen, A., Olabarriaga, S., van Vliet, L.: Gridifying a diffusion tensor imaging analysis pipeline. In: 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid), pp. 733–738 (2010)

  12. Camarasu-Pop, S., Glatard, T., Moscicki, J.T., Benoit-Cattin, H., Sarrut, D.: Dynamic partitioning of GATE Monte-Carlo simulations on EGEE. J. Grid Computing 8(2), 241–259 (2010)

    Article  Google Scholar 

  13. Casajus, A., Graciani, R., Paterson, S., Tsaregorodtsev, A., the Lhcb Dirac Team: Dirac pilot framework and the dirac workload management system. J. Phys.: Conf. Ser. 219(6), 062,049 (2010)

    Article  Google Scholar 

  14. DTI Preprocessing on the e-BioinfraGateway: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/PredtiUserDoc. Accessed 23 May 2012

  15. EGI Science Gateways: http://www.egi.eu/services/support/science-gateways/index.html. Accessed 23 May 2012

  16. Ferrari, T., Gaido, L.: Resources and services of the EGEE production infrastructure. J. Grid Computing 9, 119–133 (2011)

    Article  Google Scholar 

  17. Ferreira da Silva, R., Camarasu-Pop, S., Grenier, B., Hamar, V., Manset, D., Montagnat, J., Revillard, J., Balderrama, J.R., Tsaregorodtsev, A., Glatard, T.: Multi-infrastructure workflow execution for medical simulation in the Virtual Imaging Platform. In: Proceedings of HealthGrid 2011. Bristol, UK (2011)

  18. Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Ségonne, F., Salat, D.H., Busa, E., Seidman, L.J., Goldstein, J., Kennedy, D., Caviness, V., Makris, N., Rosen, B., Dale, A.M.: Automatically parcellating the human cerebral cortex. Cereb. Cortex 14(1), 11–22 (2004)

    Article  Google Scholar 

  19. FMRIB’s Diffusion Toolbox—BEDPOSTX: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html. Accessed 23 May 2012

  20. Genome Compare on the e-BioinfraGateway: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GenomeCompareUserDoc. Accessed 23 May 2012

  21. Gesing, S., Hemert, J.v., Kacsuk, P., Kohlbacher, O.: Special issue: portals for life sciences—providing intuitive access to bioinformatic tools. Concurrency Computat.: Pract. Exper. 23(3), 223–234 (2011)

    Article  Google Scholar 

  22. Glatard, T., Montagnat, J., Lingrand, D., Pennec, X.: Flexible and efficient workflow deployment of data-intensive applications on Grids with MOTEUR. Int. J. High Perform. Comput. Appl. 22(3), 347–360 (2008)

    Article  Google Scholar 

  23. Goodale, T., Jha, S., Kaiser, H., Kielmann, T., Kleijer, P., Von Laszewski, G., Lee, C., Merzky, A., Rajic, H., Shalf, J.: Saga: a simple api for Grid applications. High-level application programming on the Grid. Comput. Methods Sci. Technol. 12(1), 7–20 (2006)

    Google Scholar 

  24. Helmer, K.G., Ambite, J.L., Ames, J., Ananthakrishnan, R., Burns, G., Chervenak, A.L., Foster, I., Liming, L., Keator, D., Macciardi, F., Madduri, R., Navarro, J.P., Potkin, S., Rosen, B., Ruffins, S., Schuler, R., Turner, J.A., Toga, A., Williams, C., Kesselman, C., for the Biomedical Informatics Research Network: Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). J. Am. Med. Inform. Assoc. 18(4), 416–422 (2011)

    Article  Google Scholar 

  25. Hey, T., Tansley, S., Tolle, K. (eds.): The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research (2009)

  26. Kacsuk, P.: P-GRADE portal family for Grid infrastructures. Concurrency Computat.: Pract. Exper. 23(3), 235–245 (2011)

    Article  Google Scholar 

  27. Kim, J., Maddineni, S., Jha, S.: Building gateways for life-science applications using the dynamic application runtime environment (dare) framework. In: Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, TG ’11, pp. 38:1–38:8. ACM, New York (2011)

    Google Scholar 

  28. Kiss, T., Greenwell, P., Heindl, H., Terstyanszky, G., Weingarten, N.: Parameter sweep workflows for modelling carbohydrate recognition. J. Grid Computing 8, 587–601 (2010)

    Article  Google Scholar 

  29. Klarenbeek, P.L., Tak, P.P., van Schaik, B.D.C., Zwinderman, A.H., Jakobs, M.E., Zhang, Z., van Kampen, A.H.C., van Lier, R.A.W., Baas, F., de Vries, N.: Human T-cell memory consists mainly of unexpanded clones. Immunol. Lett. 133(1), 42–48 (2010)

    Article  Google Scholar 

  30. Korkhov, V., Krefting, D., Kukla, T., Terstyanszky, G.Z., Caan, M., Olabarriaga, S.D.: Exploring workflow interoperability tools for neuroimaging data analysis. In: Proceedings of the 6th Workshop on Workflows in Support of Large-Scale Science, WORKS ’11, pp. 87–96. ACM, New York (2011)

    Chapter  Google Scholar 

  31. Krefting, D., Bart, J., Beronov, K., Dzhimova, O., Falkner, J., Hartung, M., Hoheisel, A., Knoch, T.A., Lingner, T., Mohammed, Y., Peter, K., Rahm, E., Sax, U., Sommerfeld, D., Steinke, T., Tolxdorff, T., Vossberg, M., Viezens, F., Weisbecker, A.: MediGRID: Towards a user friendly secured Grid infrastructure. Future Gener. Comput. Syst. 25(3), 326–336 (2009)

    Article  Google Scholar 

  32. Luyf, A., van Schaik, B., de Vries, M., Baas, F., van Kampen, A., Olabarriaga, S.: Initial steps towards a production platform for DNA sequence analysis on the Grid. BMC Bioinformatics 11(1), 598 (2010)

    Article  Google Scholar 

  33. Marco, C., Fabio, C., Alvise, D., Antonia, G., Francesco, G., Alessandro, M., Moreno, M., Salvatore, M., Fabrizio, P., Luca, P., Francesco, P.: The glite workload management system. In: Abdennadher, N., Petcu, D. (eds.) Advances in Grid and Pervasive Computing. Lecture Notes in Computer Science, vol. 5529, pp. 256–268. Springer, Berlin (2009)

    Chapter  Google Scholar 

  34. Model–view–controller—Wikipedia: http://en.wikipedia.org/wiki/Model-view-controller. Accessed 23 May 2012

  35. Montagnat, J., Isnard, B., Glatard, T., Maheshwari, K., Fornarino, M.: A data-driven workflow language for Grids based on array programming principles. In: Proceedings of the 4th Workshop on Workflows in Support of Large-Scale Science (WORKS) (2009)

  36. Moscicki, J.T., Lamanna, M., Bubak, M., Sloot, P.M.A.: Processing moldable tasks on the Grid: late job binding with lightweight user-level overlay. Future Gener. Comput. Syst. 27(6), 725–736 (2011)

    Article  Google Scholar 

  37. Novotny, J., Russell, M., Wehrens, O.: GridSphere: a portal framework for building collaborations. Concurrency Computat.: Pract. Exper. 16(5), 503–513 (2004)

    Article  Google Scholar 

  38. Olabarriaga, S.D., Glatard, T., de Boer, P.T.: A virtual laboratory for medical image analysis. IEEE Trans. Inf. Technol. Biomed. 14(4), 979–985 (2010)

    Article  Google Scholar 

  39. Olabarriaga, S.D., Glatard, T., Boulebiar, K., de Boer, P.T.: From “low hanging” to “user ready”: initial steps into a HealthGrid. In: Global Healthgrid: e-Science Meets Biomedical Informatics—Proceedings of HealthGrid 2008, vol. 138, pp. 70–79 (2008)

  40. Pandey, S., Voorsluys, W., Rahman, M., Buyya, R., Dobson, J.E., Chiu, K.: A Grid workflow environment for brain imaging analysis on distributed systems. Concurrency Computat.: Pract. Exper. 21(16), 2118–2139 (2009)

    Article  Google Scholar 

  41. Peters, B.D., Machielsen, M.W.J., Hoen, W.P., Caan, M.W.A., Malhotra, A.K., Szeszko, P.R., Duran, M., Olabarriaga, S.D., de Haan, L.: Polyunsaturated fatty acid concentration predicts myelin integrity in earlyphase psychosis. Schizophr. Bull. (2012). doi:10.1093/schbul/sbs089

    Google Scholar 

  42. Redolfi, A., McClatchey, R., Anjum, A., Zijdenbos, A., Manset, D., Barkhof, F., Spenger, C., Legré, Y., Wahlund, L.O., di San Pietro, C.B., Frisoni, G.B.: Grid infrastructures for computational neuroscience: the neuGRID example. Future Neurol. 4(6), 703–722 (2009)

    Article  Google Scholar 

  43. Shahand, S., Caan, M., van Kampen, A., Olabarriaga, S.: Integrated support for neuroscience research: from study design to publication. In: Proceedings of HealthGrid 2012. Amsterdam, NL (2012)

  44. Shahand, S., Santcroos, M., Mohammed, Y., Korkhov, V., Luyf, A., van Kampen, A., Olabarriaga, S.: Front-ends to biomedical data analysis on Grids. In: Proceedings of HealthGrid 2011. Bristol, UK (2011)

  45. Stewart, G.A., Cameron, D., Cowan, G.A., McCance, G.: Storage and data management in egee. In: Proceedings of the fifth Australasian symposium on ACSW frontiers, vol. 68, ACSW ’07, pp. 69–77. Australian Computer Society, Inc., Darlinghurst, Australia (2007)

    Google Scholar 

  46. The BigGrid Project: http://www.biggrid.nl. Accessed 23 May 2012

  47. The Engineframe Project: http://www.enginframe.com. Accessed 23 May 2012

  48. The gLite Project: http://glite.cern.ch. Accessed 23 May 2012

  49. The Google Web Toolkit. https://developers.google.com/web-toolkit. Accessed 23 May 2012

  50. The Hibernate Project: http://www.hibernate.org. Accessed 23 May 2012

  51. The Liferay Project: http://www.liferay.com. Accessed 23 May 2012

  52. The Pylons Project: http://www.pylonsproject.org. Accessed 23 May 2012

  53. The Spring Project: http://www.springsource.org. Accessed 23 May 2012

  54. Using an Aladdin eToken PRO to store Grid certificates: http://www.nikhef.nl/pub/projects/grid/gridwiki/index.php/EToken. Accessed 23 May 2012

  55. van Wingen, G.A., Geuze, E., Caan, M.W.A., Kozicz, T., Olabarriaga, S.D., Denys, D., Vermetten, E., Fernández, G.: Persistent and reversible consequences of combat stress on the mesofrontal circuit and cognition. Proc. Natl. Acad. Sci. (PNAS) (2012). doi:10.1073/pnas.1206330109

    Google Scholar 

  56. Wilkins-Diehr, N., Gannon, D., Klimeck, G., Oster, S., Pamidighantam, S.: TeraGrid science gateways and their impact on science. Comput. 41(11), 32 –41 (2008)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Bioinformatics Laboratory, Department of Clinical Epidemiology Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    Shayan Shahand, Mark Santcroos, Antoine H. C. van Kampen & Sílvia Delgado Olabarriaga

  2. Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands

    Antoine H. C. van Kampen

Authors
  1. Shayan Shahand
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mark Santcroos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Antoine H. C. van Kampen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sílvia Delgado Olabarriaga
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sílvia Delgado Olabarriaga.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shahand, S., Santcroos, M., van Kampen, A.H.C. et al. A Grid-Enabled Gateway for Biomedical Data Analysis. J Grid Computing 10, 725–742 (2012). https://doi.org/10.1007/s10723-012-9233-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10723-012-9233-4

Keywords

Search

Navigation