Solutions for biomedical grid computing-Case studies from the D-Grid project Services@MediGRID

Journal of Computational Science

Volumn 3, Issue 5, 2012, Pages 280-297

  Dickmann, Frank ^a   Falkner, Jürgen ^b   Gunia, Wilfried ^c   Hampe, Jochen ^d   Hausmann, Michael ^e   Herrmann, Alexander ^d   Kepper, Nick ^e,f   Knoch, Tobias A ^f,g   Lauterbach, Svenja ^h   Lippert, Jörg ⁱ   Peter, Kathrin ^j   Schmitt, Eberhard ^e   Schwardmann, Ulrich ^k   Solodenko, Juri ⁱ   Sommerfeld, Dietmar ^k   Steinke, Thomas ^j   Weisbecker, Anette ^b   Sax, Ulrich ^a  

^a UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^b FRAUNHOFER IAO   (Germany)

^c UNIVERSITY OF COLOGNE   (Germany)

^d UNIVERSITY OF KIEL   (Germany)

^e UNIVERSITY OF HEIDELBERG   (Germany)

^f GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^g ERASMUS MEDICAL CENTER   (Netherlands)

^h Carus AG   (Germany)

ⁱ BAYER AG   (Germany)

^j ZUSE INSTITUTE BERLIN   (Germany)

^k Gessellschaft für Wissenschaftliche Datenverarbeitung mbH Göttingen   (Germany)

more..

Author keywords

Grid business concepts; Grid based tool set for genetics; Healthgrids; MediGRID; Services@MediGRID

Indexed keywords

GRID BUSINESS CONCEPTS; GRID-BASED; HEALTHGRIDS; MEDIGRID; SERVICES@MEDIGRID;

DATA VISUALIZATION; TECHNOLOGY TRANSFER;

GRID COMPUTING;

EID: 84865360567     PISSN: 18777503     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jocs.2011.06.006     Document Type: Article

References (83)

1. D-Grid Initiative, (accessed 26.01.09). http://www.d-grid.de/.
2. Services@MediGRID, (accessed 12.10.08). http://services.medigrid.de/.
3. Dickmann F., Kaspar M., Löhnhardt B., Knoch T.A., Sax U. Perspectives of MediGRID. Studies in Health Technology and Informatics 2009, 147:173-182.
4. 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 Generation Computer Systems 2009, 25(3):326-336.
5. Sheshabalaya T. Grid computing and E-health. Healthcare IT Management 2010, 5(1):16-19.
6. Dickmann F., Brodhun M., Falkner J., Knoch T.A., Sax U. Technology transfer of dynamic IT outsourcing requires security measures in SLAs, economics of grids, clouds, systems, and services. 7th International Workshop, GECON 2010 2010, 1-15.
7. Foster I. Globus toolkit version 4: software for service-oriented systems. Journal of Computer Science and Technology 2006, 21(4):513-520.
8. Hoheisel A. Grid workflow execution service - dynamic and interactive execution and visualization of distributed workflows. Proceedings of the Cracow Grid Workshop 2006.
9. Wieczorek M., Hoheisel A., Prodan R. Towards a general model of the multi-criteria workflow scheduling on the grid. Future Generation Computer Systems 2009, 25(3):237-256.
10. Stanoevska-Slabeva K., Wozniak T. Cloud basics - an introduction to cloud computing. Grid and Cloud Computing 2009, 47-62. Springer, Heidelberg. K. Stanoevska-Slabeva, T. Wozniak, S. Ristol (Eds.).
11. Sommerfeld D., Lingner T., Stanke M., Morgenstern B., Richter H. AUGUSTUS at MediGRID: adaption of a bioinformatics application to grid computing for efficient genome analysis. Future Generation Computer Systems 2009, 25(3):337-345.
12. Chakrabarti A. Grid Computing Security 2007, Springer, Berlin/Heidelberg/New York.
13. Foster I., Zhao Y., Raicu I., Lu S. Cloud computing and grid computing 360-degree compared. IEEE Grid Computing Environments (GCE08) 2008, 1-10.
14. The Distributed Grid Accounting System (DGAS), (accessed 08.05.09). http://www.to.infn.it/grid/accounting/main.html.
15. SRB - The DICE Storage Resource Broker, (accessed 19.10.10). http://www.sdsc.edu/srb/index.php.
16. Rajasekar A., Wan M., Moore R., Schroeder W., Kremenek G., Jagatheesan A., Cowart C., Zhu B., Chen S., Olschanowsky R. Storage resource broker-managing distributed data in a grid. Computer Society of India Journal 2003, 33(4):42-54. special issue on SAN.
17. Rajasekar A., Wan M., Moore R., Schroeder W. A prototype rule-based distributed data management system. HPDC Workshop on Next-Generation Distributed Data Management 2006.
18. iRODS - The Integrated Rule-Oriented Data System, (accessed 19.10.10). https://www.irods.org/.
19. Rajasekar A., Moore R., Hou C., Lee C., Marciano R., de Torcy A., Wan M., Schroeder W., Chen S., Gilbert L. iRODS primer: integrated rule-oriented data system. Synthesis Lectures on Information Concepts, Retrieval, and Services 2010, 2(1):1-143.
20. Magoulès F. Introduction to Grid Computing 2009, CRC Press, Boca Raton.
21. Goo J., Nam K. Contract as a source of trust - commitment in successful IT outsourcing relationship: an empirical study. 40th Annual Hawaii International Conference on System Sciences (HICSS'07) 2007.
22. Wiebelitz J. Accounting im D-Grid (DGAS), Regionales Rechenzentrum für Niedersachsen (RRZN). Erster D-Grid Accounting/Billing Workshop 2008.
23. Deutscher Bundestag, BDSG vom 20.12.1990 (BGBl. I S. 2954), neugefasst durch Bek. v. 14.01.2003 (BGBl. I S. 66), zuletzt geändert durch Gesetz vom 29.07.2009 (BGBl. I S. 2254), durch Artikel 5 des Gesetzes vom 29.07.2009 (BGBl. I S. 2355 [2384]) und durch Gesetz vom 14.08.2009 (BGBl. I S. 2814), nicht amtliche Fassung (Stand: 11. Juni 2010), Der Bundesbeauftragte für den Datenschutz und die Informationsfreiheit, 2009.
24. Bundesamt für Sicherheit in der Informationstechnik, (accessed 14.10.10). http://www.bsi.bund.de/.
25. Trienekens J.J.M., Bouman J.J., Zwan M.v.d. Specification of service level agreements: problems. Principles and Practices Software Quality Journal 2004, 12(1):43-57.
26. Bozeman B. Technology transfer and public policy: a review of research and theory. Research Policy 2000, 29(4-5):627-655.
27. Stephens M., Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics 2003, 73(5):1162-1169.
28. Scheet P., Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics 2006, 78(4):629-644.
29. Voight B.F., Kudaravalli S., Wen X., Pritchard J.K. A map of recent positive selection in the human genome. PLoS Biology 2006, 4(3):e72.
30. Herold C., Steffens M., Brockschmidt F.F., Baur M.P., Becker T. INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics 2009, 25(24):3275-3281.
31. Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M., Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research 2006, 34(1):D354-D357.
32. Berg J., Willmann S., Lässig M. Adaptive evolution of transcription factor binding sites. BMC Evolutionary Biology 2004, 4(1):42.
33. Volpi E.V., Bridger J.M. FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 2008, 45(4):385-409.
34. Hausmann M., Winkler R., Hildenbrand G., Finsterle J., Weisel A., Rapp A., Schmitt E., Janz S., Cremer C. COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations. Biotechniques 2003, 35(3):564-577.
35. Schmitt E., Schwarz-Finsterle J., Stein S., Boxler C., Müller P., Mokhir A., Krämer R., Cremer C., Hausmann M. Combinatorial Oligo FISH: directed labelling of specific genome domains in differentially fixed cell material and live cells. Methods in Molecular Biology 2010, 659:185-202.
36. Schwarz-Finsterle J., Stein S., Großmann C., Schmitt E., Trakhtenbrot L., Rechavi G., Amariglio N., Cremer C., Hausmann M. Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei. Journal of Biochemical and Biophysical Methods 2007, 70(3):397-406.
37. Schwarz-Finsterle J., Stein S., Grossmann C., Schmitt E., Trakhtenbrot L., Rechavi G., Amariglio N., Cremer C., Hausmann M. COMBO-FISH for focussed fluorescence labelling of gene domains: 3D-analysis of the genome architecture of abl and bcr in human blood cells. Cell Biology International 2005, 29(12):1038-1046.
38. Schmitt E., Müller P., Stein S., Schwarz-Finsterle J., Hausmann M. Cell nucleus architecture in health and medicine: geometrical descriptors and their use in grid based case studies. Studies in Health Technology and Informatics 2010, 159:272-276.
39. Schmitt E., Stein S., Hausmann M. Conception of an image data base for cell nuclei and geometric algorithms for diagnosis and therapy monitoring. Studies in Health Technology and Informatics 2009, 147:251-256.
40. E. Schmitt, J. Wagner, M. Hausmann, Combinatorial selection of short triplex forming oligonucleotides for fluorescence in situ hybridisation COMBO-FISH, Journal of Computational Science, in this issue.
41. Grossmann C., Schwarz-Finsterle J., Schmitt E., Birk U., Hildenbrand G., Cremer C., Trakhtenbrot L., Hausmann M. Variations of the spatial fluorescence distribution in ABL gene chromatic domains measured in blood cell nuclei by SMI microscopy after COMBO-FISH labelling. Microscopy: Science, Technology, Applications and Education 2010, 688-695. Formatex Research Center, Badajoz. A. Méndez-Vilas, J. Díaz álvarez (Eds.).
42. Hausmann M., Hildenbrand G., Schwarz-Finsterle J., Birk U., Schneider H., Cremer C., Schmitt E. New technologies measure genome domains - high resolution microscopy and novel labeling procedures enable 3-D studies of the functional architecture of gene domains in cell nuclei. Biophotonics International 2005, 12(10):34-37.
43. Lemmer P., Gunkel M., Baddeley D., Kaufmann R., Urich A., Weiland Y., Reymann J., Müller P., Hausmann M., Cremer C. SPDM: light microscopy with single-molecule resolution at the nanoscale. Applied Physics B: Lasers and Optics 2008, 93(1):1-12.
44. Lemmer P., Gunkel M., Weiland Y., Müller P., Baddeley D., Kaufmann R., Urich A., Eipel H., Amberger R., Hausmann M. Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. Journal of Microscopy 2009, 235(2):163-171.
45. Bohn M., Diesinger P., Kaufmann R., Weiland Y., Müller P., Gunkel M., von Ketteler A., Lemmer P., Hausmann M., Heermann D.W., Cremer C. Localization microscopy reveals expression-cependent parameters of chromatin nanostructure. Biophysical Journal 2010, 99(5):1358-1367.
46. Müller P., Schmitt E., Jacob A., Hoheisel J., Kaufmann R., Cremer C., Hausmann M. COMBO-FISH enables high precision localization microscopy as a prerequisite for nanostructures analysis of genome loci. International Journal of Molecular Sciences 2010, 10(11):4094-4105.
47. Hildenbrand G., Rapp A., Spöri U., Wagner C., Cremer C., Hausmann M. Nano-sizing of specific gene domains in intact human cell nuclei by spatially modulated illumination light microscopy. Biophysical Journal 2005, 88(6):4312-4318.
48. Wiech T., Stein S., Lachenmaier V., Schmitt E., Schwarz-Finsterle J., Wiech E., Hildenbrand G., Werner M., Hausmann M. Spatial allelic imbalance of BCL2 genes and chromosome 18 territories in nonneoplastic and neoplastic cervical squamous epithelium. European Biophysics Journal 2009, 38(6):793-806.
49. Timme S., Schmitt E., Stein S., Schwarz-Finsterle J., Wagner J., Walch A., Werner M., Hausmann M., Wiech T. Nuclear position and shape deformation of chromosome 8 territories in pancreatic ductal adenocarcinoma. Analytical Cellular Pathology 2011, 34:21-33.
50. Cremer T., Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Reviews Genetics 2001, 2(4):292-301.
51. Jhunjhunwala S., van Zelm M.C., Peak M.M., Cutchin S., Riblet R., van Dongen J.J.M., Grosveld F.G., Knoch T.A., Murre C. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions for long-range genomic interactions. Cell 2008, 133(2):265-279.
52. Knoch T.A. Approaching the Three-Dimensional Organization of the Human Genome: Structural-, Scaling- and Dynamic Properties in the Simulation of Interphase Chromosomes and Cell Nuclei, Long-Range Correlations in Complete Genomes, In Vivo Quantification of the Chromatin Distribution Construct Conversions in Simultaneous Co-transfections 2002, Combined Faculties for the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg, Germany, Heidelberg.
53. Knoch T.A. Towards a holistic understanding of the human genome by determination and integration of its sequential and three-dimensional organization. High Performance Computing in Science and Engineering'03: Transactions of the High Performance Computing Center 2003, 421.
54. Flicek P., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., Down T., Dyer S.C., Eyre T., Fitzgerald S., Fernandez-Banet J., Gräf S., Haider S., Hammond M., Holland R., Howe K.L., Howe K., Johnson N., Jenkinson A., Kähäri A., Keefe D., Kokocinski F., Kulesha E., Lawson D., Longden I., Megy K., Meidl P., Overduin B., Parker A., Pritchard B., Prlic A., Rice S., Rios D., Schuster M., Sealy I., Slater G., Smedley D., Spudich G., Trevanion S., Vilella A.J., Vogel J., White S., Wood M., Birney E., Cox T., Curwen V., Durbin R., Fernandez-Suarez X.M., Herrero J., Hubbard T.J.P., Kasprzyk A., Proctor G., Smith J., Ureta-Vidal A., Searle S. Ensembl 2008. Nucleic Acids Research 2008, 36(Suppl. 1):D707-D714.
55. Bernardi G. The human genome: organization and evolutionary history. Annual Review of Genetics 1995, 29(1):445-476.
56. Karolchik D., Kuhn R.M., Baertsch R., Barber G.P., Clawson H., Diekhans M., Giardine B., Harte R.A., Hinrichs A.S., Hsu F., Kober K.M., Miller W., Pedersen J.S., Pohl A., Raney B.J., Rhead B., Rosenbloom K.R., Smith K.E., Stanke M., Thakkapallayil A., Trumbower H., Wang T., Zweig A.S., Haussler D., Kent W.J. The UCSC genome browser database: 2008 update. Nucleic Acids Research 2008, 36(Suppl. 1):D773-D779.
57. Elnitski L.L., Shah P., Moreland R.T., Umayam L., Wolfsberg T.G., Baxevanis A.D. The ENCODEdb portal: simplified access to ENCODE consortium data. Genome Research 2007, 17(6):954-959.
58. Butler D. Virtual globes: the web-wide world. Nature 2006, 439(7078):776-778.
59. Couture L.A., Rashid H. Asymptote Flux 2002, Phaidon Press, Hereford, UK.
60. Gerstein M. Tools needed to navigate landscape of the genome. Nature 2006, 440(7085):740.
61. Knoch T.A., Lesnussa M., Kepper N., Eussen H.B., Grosveld F.G. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function. Studies in Health Technology and Informatics 2009, 147:105-116.
62. Sax U., Weisbecker A., Falkner J., Viezens F., Mohammed Y., Hartung M., Bart J., Krefting D., Knoch T.A., Semler S.C. Grid-basierte Services für die elektronische Patientenakte der Zukunft. E-HEALTH-COM 2007, 2(4):61-63.
63. Sax U., Weisbecker A., Falkner J., Viezens F., Mohammed Y., Hartung M., Bart J., Krefting D., Knoch T.A., Semler S.C. Auf dem Weg zur individualisierten Medizin - Grid-basierte Services für die EPA der Zukunft, Telemed 2007 - Electronic Health Record und Gesundheitsportale, Berlin 2008, pp. 47-51.
64. de Zeeuw L.V., Knoch T.A., van den Berg J., Grosveld F.G. Erasmus computing grid - Het bouwen van een 20 TeraFLOP virtuelle supercomputer. NIOC Proceedings 2007 - Het Perspective of lange termijn 2007.
65. Knoch T.A., Baumgärtner V., Grosveld F.G., Egger K. Approaching the internalization challenge of grid technologies into e-society by e-human "grid" ecology, economics of grids, clouds, systems, and services. 7th International Workshop, GECON 2010 2010, 116-128.
66. Hampe J., Franke A., Rosenstiel P., Till A., Teuber M., Huse K., Albrecht M., Mayr G., De La Vega F.M., Briggs J., Gunther S., Prescott N.J., Onnie C.M., Hasler R., Sipos B., Folsch U.R., Lengauer T., Platzer M., Mathew C.G., Krawczak M., Schreiber S. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nature Genetics 2007, 39(2):207-211.
67. Buch S., Schafmayer C., Volzke H., Becker C., Franke A., von Eller-Eberstein H., Kluck C., Bassmann I., Brosch M., Lammert F., Miquel J.F., Nervi F., Wittig M., Rosskopf D., Timm B., Holl C., Seeger M., ElSharawy A., Lu T., Egberts J., Fandrich F., Folsch U.R., Krawczak M., Schreiber S., Nurnberg P., Tepel J., Hampe J. A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease. Nature Genetics 2007, 39(8):995-999.
68. Franke A., Wollstein A., Teuber M., Wittig M., Lu T., Hoffmann K., Nuernberg P., Krawczak M., Schreiber S., Hampe J. GENOMIZER: an integrated analysis system for genome-wide association data. Human Mutation 2006, 27(6):583-588.
69. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009, 10(1):57-63.
70. Nothnagel M., Wolf A., Herrmann A., Szafranski K., Vater I., Brosch M., Huse K., Siebert R., Platzer M., Hampe J., Krawczak M. Statistical inference of allelic imbalance from transcriptome data. Human Mutation 2011, 32:98-106.
71. Willmann S., Lippert J., Schmitt W. From physicochemistry to absorption and distribution: predictive mechanistic modelling and computational tools. Expert Opin Drug Metab Toxicol 2005, 1(1):159-168.
72. Vossen M., Sevestre M., Niederalt C., Jang I., Willmann S., Edginton A. Dynamically simulating the interaction of midazolam and the CYP3A4 inhibitor itraconazole using individual coupled whole-body physiologically-based pharmacokinetic (WB-PBPK) models. Theoretical Biology and Medical Modelling 2007, 4:13.
73. Willmann S., Edginton A., Coboeken K., Ahr G., Lippert J. Risk to the breast-fed neonate from codeine treatment to the mother: a quantitative mechanistic modeling study. Clinical Pharmacology & Therapeutics 2009, 86(6):634-643.
74. Edginton A., Willmann S. Physiology-based simulations of a pathological condition: prediction of pharmacokinetics in patients with liver cirrhosis. Clinical Pharmacokinetics 2008, 47(11):743-752.
75. Willmann S., Höhn K., Edginton A., Sevestre M., Solodenko J., Weiss W., Lippert J., Schmitt W. Development of a physiology-based whole-body population model for assessing the influence of individual variability on the pharmacokinetics of drugs. Journal of Pharmacokinetics and Pharmacodynamics 2007, 34(3):401-431.
76. Bayer Technology Services, Computational Systems Biology Software Suite, (accessed 20.10.10). http://www.systems-biology.com/products.html.
77. Altmann J., Courcoubetis C., Stamoulis G.D., Dramitinos M., Rayna T., Risch M., Bannink C. GridEcon: a market place for computing resources grid economics and business models. 5th International Workshop, GECON 2008 2008.
78. Dickmann F., Kaspar M., Löhnhardt B., Kepper N., Viezens F., Hertel F., Lesnussa M., Mohammed Y., Thiel A., Steinke T., Bernarding J., Krefting D., Knoch T.A., Sax U. Visualization in health grid environments: a novel service and business approach grid economics and business models. 6th International Workshop, GECON 2009 2009, 150-159.
79. Buyya R., Abramson D., Venugopal S. The grid economy. Proceedings of the IEEE 2005, 93(3):698-714.
80. Falkner J., Weisbecker A. Engineering of services and business models for grid applications grid economics and business models. 6th International Workshop, GECON 2009 2009.
81. Stanoevska-Slabeva K., Parrilli D.M., Thanos G. BEinGRID: development of business models for the grid industry grid economics and business models. 5th International Workshop, GECON 2008 2008.
82. WissGrid, (accessed 15.08.09). http://www.wissgrid.de/.
83. Marincola F.M. Translational medicine: a two-way road. Journal of Translational Medicine 2003, 1(1):1-2.