The virtual kidney: An eScience interface and Grid portal

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 367, Issue 1896, 2009, Pages 2141-2159

  Harris, Peter J ^a   Buyya, Rajkumar ^b   Chu, Xingchen ^b   Kobialka, Tom ^b   Kazmierczak, Ed ^b   Moss, Robert ^b   Appelbe, William ^c   Hunter, Peter J ^d   Thomas, S Randall ^e  

^a Faculty of Medicine Dentistry and Health Sciences   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c Victorian Partnership for Advanced Computing   (Australia)

^d UNIVERSITY OF AUCKLAND   (New Zealand)

^e UNIVERSITY OF EVRY   (France)

Author keywords

Computational biology; Cyberinfrastructure; Grid computing; Kidney modelling; Physiome; Three dimensional anatomical visualization

Indexed keywords

BIOINFORMATICS; BIOLOGY; BLOOD VESSELS; COMPUTER SCIENCE; DATABASE SYSTEMS; MATHEMATICAL MODELS; PLANNING; RESEARCH; RESOURCE ALLOCATION; SIMULATORS; TELECOMMUNICATION SYSTEMS; THREE DIMENSIONAL; VISUALIZATION;

COMPUTATIONAL BIOLOGY; CYBERINFRASTRUCTURE; KIDNEY MODELLING; PHYSIOME; THREE-DIMENSIONAL ANATOMICAL VISUALIZATION;

GRID COMPUTING;

ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; INTERNET; KIDNEY; PHYSIOLOGY;

COMPUTER GRAPHICS; INTERNET; KIDNEY; MODELS, BIOLOGICAL; USER-COMPUTER INTERFACE;

EID: 67650908450     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2008.0291     Document Type: Article

References (40)

1. Alfieri, R., Cecchini, R., Ciaschini, V., dell'Agnello, L., Frohner, Á . & Gianoli, A. 2003 VOMS: an authorization system for virtual organizations. In First European Across Grids Conference, Santiago de Compostela.
2. Baru, C., Moore, R., Rajasekar, A. & Wan, M. 1998 The SDSC storage resource broker. In Proc. CASCON'98, Toronto, Canada.
3. Bassingthwaighte, J. B. 2000 Strategies for the Physiome Project. Ann. Biomed. Eng. 28, 1043-1058. (doi:10.1114/1.1313771)
4. Chang, H. & Fujita, T. 1999 A numerical model of the renal distal tubule. Am. J. Physiol. 276, F931-F951.
5. Christie, R., Bullivant, D., Blackett, S. & Hunter, P. J. 2002 Modelling and visualising the heart. Comput. Vis. Sci. 4, 227-235. (doi:10.1007/s00791-002-0079-3)
6. Chu, X.-C., Lonie, A., Harris, P. J., Thomas, S. R. & Buyya, R. 2008 A service-oriented Grid environment for integration of distributed kidney models and resources. Concurrency Comput. Pract. Exp. 20, 1095-1111. (doi:10.1002/cpe.1285)
7. Deen, W. M., Robertson, C. R. & Brenner, B. M. 1972 A model of glomerular ultrafiltration in the rat. Am. J. Physiol. 223, 1178-1183.
8. Dzodic, V., Hervy, S., Fritsch, D., Khalfallah, H., Thereau, M. & Thomas, S. R. 2004 Web-based tools for quantitative renal physiology. Cell. Mol. Biol. 50, 795-800.
9. Fenner, J. W. et al. 2008 The EuroPhysiome, STEP and a roadmap for the virtual physiological human. Phil. Trans. R. Soc. A 366, 2979-2999. (doi:10.1098/rsta.2008.0089)
10. Foster, D. M. & Jacquez, J. A. 1978 Comparison using central core model of renal medulla of the rabbit and rat. Am. J. Physiol. 234, F402-F414.
11. Foster, I. & Kesselman, C. 1998 The Globus Project: a status report. In Proc. IPPS/SPDP'98 Heterogeneous Computing Workshop, pp. 4-18.
12. Foster, I. & Kesselman, C. 1999 The Grid: blueprint for a future computing infrastructure. San Francisco, CA: Morgan Kaufmann Publishers.
13. Hervy, S. & Thomas, S. R. 2003 Inner medullary lactate production and urine-concentrating mechanism: a flat medullary model. Am. J. Physiol. Renal Physiol. 284, F65-F81.
14. Holstein-Rathlou, N. H. & Marsh, D. J. 1990 A dynamic model of the tubuloglomerular feedback mechanism. Am. J. Physiol. 258, F1448-F1459.
15. Holstein-Rathlou, N. H., Wagner, A. J. & Marsh, D. J. 1991 Tubuloglomerular feedback dynamics and renal blood flow autoregulation in rats. Am. J. Physiol. 260, F53-F68.
16. Hunter, P. J. & Borg, T. K. 2003 Integration from proteins to organs: the Physiome Project. Nat. Rev. Mol. Cell Biol. 4, 237-243. (doi:10.1038/nrm1054)
17. Hunter, P. J. & Nielsen, P. M. F. 2005 A strategy for integrative computational physiology. Physiology 20, 316-325. (doi:10.1152/physiol.00022.2005)
18. Layton, H. E., Pitman, E. B. & Moore, L. C. 1991 Bifurcation analysis of TGF-mediated oscillations in SNGFR. Am. J. Physiol. 261, F904-F919.
19. Lifton, R. P., Gharavi, A. G. & Geller, D. S. 2001 Molecular mechanisms of human hypertension. Cell 104, 545-556. (doi:10.1016/S0092-8674(01)00241-0)
20. Lloyd, C. M., Halstead, M. D. B. & Nielsen, P. M. F. 2004 CellML: its future, present and past. Prog. Biophys. Mol. Biol. 85, 433-450. (doi:10.1016/j.pbiomolbio.2004.01.004)
21. Lonie, A. J., Stevens, C. & Harris, P. J. 2004 Computer modeling of kidney function. In Proc. Exp. Biol. LB520, Washington, DC.
22. Lory, P. 1987 Effectiveness of a salt transport cascade in the renal medulla: computer simulations. Am. J. Physiol. 252, F1095-F1102.
23. Marsh, D. J., Sosnovtseva, O. V., Mosekilde, E. & Holstein-Rathlou, N.-H. 2007 Vascular coupling induces synchronization, quasiperiodicity, and chaos in a nephron tree. Chaos 17. 015 114. (doi:10.1063/1. 2404774)
24. Moss, R., Kazmierczak, E., Kirley, M. & Harris, P. 2009 A computational model for emergent dynamics in the kidney. Phil. Trans. R. Soc. A 367, 2125-2140. (doi:10.1098/rsta.2008.0313)
25. Noble, D. 2002 The rise of computational biology. Nat. Rev. Mol. Cell Biol. 3, 459-463. (doi:10. 1038/nrm810)
26. Nordsletten, D., Blacket, S., Bentley, M., Ritman, E. & Smith, N. P. 2006 Structural morphology of renal vasculature. Am. J. Physiol. 291, H296-H309. (doi:10.1152/ajpheart.00814.2005)
27. Ribba, B., Tracqui, P., Boix, J. L., Boissel, J. P. & Thomas, S. R. 2006 QxDB: a generic database to support mathematical modelling in biology. Phil. Trans. R. Soc. A 364, 1517-1532. (doi:10. 1098/rsta.2006.1784)
28. Stein, L. D. 2008 Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat. Rev. (Genet.) 9, 678-688. (doi:10.1038/nrg2414)
29. Stephenson, J. L., Mejia, R. & Tewarson, R. P. 1976 Model of solute and water movement in the kidney. Proc. Natl Acad. Sci. USA 73, 252-256. (doi:10.1073/pnas.73.1.252)
30. Stephenson, J., Zhang, Y., Eftekhari, A. & Tewarson, R. 1987 Electrolyte transport in a centralcore model of the renal medulla. Am. J. Physiol. 253, F982-F997.
31. Thomas, S. R. 1991 Effect of varying salt and urea permeabilities along descending limbs of Henle in a model of the renal medullary urine concentrating mechanism. Bull. Math. Biol. 53, 825-843. (doi:10.1016/S0092- 8240(05)80409-4)
32. Thomas, S. R. In press. Kidney modeling and systems physiology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine.
33. Thomas, S. R. & Dagher, G. 1994 A kinetic model of rat proximal tubule transport-loaddependent bicarbonate reabsorption along the tubule. Bull. Math. Biol. 56, 431-458.
34. Thomas, S. R. et al. 2008 SAPHIR: a Physiome core model of body fluid homeostasis and blood pressure regulation. Phil. Trans. R. Soc. A 366, 3175-3197. (doi:10.1098/rsta.2008.0079)
35. Tripodi, G., Florio, M., Ferrandi, M., Modica, R., Zimdahl, H., Hubner, N., Ferrari, P. & Bianchi, G. 2004 Effect of Add1 gene transfer on blood pressure in reciprocal congenic strains of Milan rats. Biochem. Biophys. Res. Commun. 324, 562-568. (doi:10.1016/j.bbrc.2004.09.079)
36. Venugopal, S., Buyya, R. & Winton, L. 2004 A Grid service broker for scheduling distributed dataoriented applications on global grids. In Proc. 2nd Int. Workshop on Middleware for Grid Computing. New York, NY: ACM Press.
37. Weinstein, A. M. 1986 A mathematical model of the rat proximal tubule. Am. J. Physiol. 250, F860-F873.
38. Weinstein, A. M. 1994 Mathematical models of tubular transport. Annu. Rev. Physiol. 56, 691-709. (doi:10.1146/annurev.ph.56.030194.003355)
39. Weinstein, A. M. 1998a Insights from mathematical modeling of renal tubular function. Exp. Nephrol. 6, 462-468. (doi:10.1159/000020556)
40. Weinstein, A. M. 1998b A mathematical model of the inner medullary collecting duct of the rat-acid/base transport. Am. J. Physiol. 43, F856-F867.