A Grid-Enabled Gateway for Biomedical Data Analysis

Journal of Grid Computing

Volumn 10, Issue 4, 2012, Pages 725-742

  Shahand, Shayan ^a   Santcroos, Mark ^a   van Kampen, Antoine H C ^a,b   Olabarriaga, Sílvia Delgado ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Biomedical research; E science; Grid computing; Grid user interface; Grid web portal; Scientific gateway

Indexed keywords

BIOMEDICAL DATA; BIOMEDICAL RESEARCH; BIOMEDICAL SCIENCE; DATA ANALYSIS METHODS; E-SCIENCE; GRID COMPUTING TECHNOLOGY; GRID INFRASTRUCTURES; LARGE SCALE DATA; MEDICAL STUDENTS; RESEARCH PROBLEMS; WEB-BASED INTERFACE; WORKFLOW MANAGEMENTS;

MIDDLEWARE; MULTIMEDIA SYSTEMS; RESEARCH; USER INTERFACES; WORK SIMPLIFICATION;

GRID COMPUTING;

EID: 84871662510     PISSN: 15707873     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10723-012-9233-4     Document Type: Article

References (56)

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