High-throughput cardiac science on the grid

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

Volumn 368, Issue 1925, 2010, Pages 3907-3923

  Abramson, David ^a   Bernabeu, Miguel O ^b   Bethwaite, Blair ^a   Burrage, Kevin ^b   Corrias, Alberto ^b   Enticott, Colin ^a   Garic, Slavisa ^a   Gavaghan, David ^b   Peachey, Tom ^a   Pitt Francis, J ^b   Pueyo, E ^b   Rodriguez, Blanca ^b   Sher, Anna ^b   Tan, Jefferson ^a  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bio engineering; Cardiac science; E Science; Grid computing

Indexed keywords

ELECTROPHYSIOLOGY; GRID COMPUTING; HEART;

ACTION POTENTIALS; BIO-ENGINEERING; CARDIAC CELL; CARDIAC ELECTROPHYSIOLOGY; CARDIAC SCIENCE; CARDIAC TISSUES; CELLULAR LEVELS; COMPLEX MODEL; CRITICAL ISSUES; CURRENT MODELS; DETAILED MODELS; E-SCIENCE; ELECTRICAL ACTIVITIES; HIGH-PERFORMANCE PLATFORMS; HIGH-THROUGHPUT; MODEL OUTPUTS; OVERFITTING; PARAMETRIC MODELLING; PHYSIOLOGICAL EFFECTS; SINGLE-ION CHANNELS;

PHYSIOLOGICAL MODELS;

ACTION POTENTIAL; ARTICLE; BIOENGINEERING; BIOLOGICAL MODEL; COMPUTER; COMPUTER ANALYSIS; COMPUTER PROGRAM; CYTOLOGY; ELECTROPHYSIOLOGY; HEART; HEART MUSCLE; HEART VENTRICLE; HISTOLOGY; HUMAN; METHODOLOGY; PHYSIOLOGY;

ACTION POTENTIALS; BIOENGINEERING; COMPUTERS; COMPUTING METHODOLOGIES; ELECTROPHYSIOLOGY; HEART; HEART VENTRICLES; HUMANS; MODELS, BIOLOGICAL; MYOCARDIUM; SOFTWARE;

EID: 77956454644     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2010.0170     Document Type: Article

References (31)

1. Abramson, D., Sosic, R., Giddy, J. & Hall, B. 1995 Nimrod: A tool for performing parametrised simulations using distributed workstations. In Proc. 4th IEEE Int. Symp. on High Performance Distributed Computing (HPDC 1995), Pentagon City, VA, 1-4 August, pp. 112-121. New York, NY: IEEE Computer Society. (doi:10.1109/HPDC.1995.518701)
2. Abramson, D., Lewis, A. & Peachy, T. 2000a Nimrod/O: A tool for automatic design optimization. In Algorithms and Architectures for Parallel Processing (ICA3PP), Proc. 4th Int. Conf., Hong Kong, 11-13 December (eds A. Goscinski, H. H. Ip & W. Jia). Singapore: World Scientific.
3. Abramson, D., Giddy, J. & Kotler, L. 2000b High performance parametric modeling with Nimrod/G: Killer application for the global grid? In Proc. 14th Int. Parallel and Distributed Processing Symp. (IPDPS'00), Cancun, Mexico, 1-5 May, pp. 520-528. Los Alamitos, CA: IEEE Computer Society. (doi:10.1109/IPDPS.2000.846030)
4. Abramson, D., Lewis, A., Peachey, T. & Fletcher, C. 2001 An automatic design optimization tool and its application to computational fluid dynamics. In Proc. 2001 ACM/IEEE Conf. on Supercomputing, Denver, CO, 10-16 November, paper 47. Los Alamitos, CA: IEEE Computer Society. (doi:10.1109/SC.2001.10054)
5. Abramson, D., Enticott, C. & Altintas, I. 2008 Nimrod/K: Towards massively parallel dynamic grid workflows. In Proc. 2008 ACM/IEEE Conf. on Supercomputing, Austin, TX, 15-21 November. New York, NY: ACM. (doi:10.1145/1413370.1413395)
6. Abramson, D., Bethwaite, B., Enticott, C., Garic, S., Peachey, T., Michailova, A, Amirriazi, S. & Chitters, R. 2009 Robust workflows for science and engineering. In Proc. 2nd Workshop on Many-Task Computing on Grids and Supercomputers, at Conf. on High Performance Networking and Computing, Portland, OR, 16 November. New York, NY: ACM. (doi:10.1145/1646468. 1646469)
7. Altintas, I., Birnbaum, A., Baldridge, K., Sudholt, W., Miller, M., Amoreira, C., Potier, Y. & Ludaescher, B. 2005 A framework for the design and reuse of grid workflows. In Scientific Applications of Grid Computing, First Int. Workshop (SAG 2004), Beijing, China, 20-24 September 2004. Lecture Notes in Computer Science, no. 3458, pp. 120-133. Berlin, Germany: Springer. (doi:10.1007/11423287-11)
8. Bernabeu, M., Bishop, M., Pitt-Francis, J., Gavaghan, D., Grau, V. & Rodriguez, B. 2008 High performance computer simulations for the study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para-cellular resolution. In Computers in Cardiology 2008, Bologna, Italy, 14-17 September, vol. 35, pp. 721-724. See http://www.cinc. org/archives/2008/pdf/0721.pdf.
9. Bernabeu, M. O. et al. 2009a Grid computing simulations of ion channel block effects on the ECG using 3D anatomically-based models. In Computers in Cardiology 2009, Park City, UT, 13-16 September, vol. 36, pp. 213-216. See http://www.cinc.org/archives/2009/pdf/0213.pdf.
10. Bernabeu, M. O. et al. 2009b CHASTE: Incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library. Phil. Trans. R. Soc. A 367, 1907-1930. (doi:10.1098/rsta.2008.0309)
11. Capener, C. E., Kim, H. J., Arinaminpathy, Y. & Sansom, M. S. P. 2002 Ion channels: Structural bioinformatics and modelling. Human Mol. Genet. 11, 2425-2433. (doi:10.1093/hmg/11.20.2425)
12. Cary, J. R., Shasharina, S. G., Cummings, J. C., Reynders, J. V. & Hinker, P. J. 1997 Comparison of C++ and Fortran 90 for object-oriented scientific programming. Comput. Phys. Commun. 105, 20-36. (doi:10.1016/S0010- 4655(97)00043-X)
13. Cooper, J., McKeever, S. & Garny, A. 2006 On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations, pp. 12-20. New York, NY: ACM.
14. +]i overloaded cardiac myocytes: A simulation study. Biophys. J. 78, 2392-2404. (doi:10.1016/S0006-3495(00)76783-X)
15. Fitton, A. & Sorkin, E. M. 1993 Sotalol: An updated review of its pharmacological properties and therapeutic use in cardiac arrhythmias. Drugs 46, 678-719. (doi:10.2165/00003495-199346040-00007)
16. Foster, I. & Kesselman, C. (eds) 2003 The grid: Blueprint for a new computing infrastructure, 2nd edn. Los Altos, CA: Morgan Kaufmann.
17. Goscinski, W. & Abramson, D. 2005 Application deployment over heterogeneous grids using distributed ant. In Proc. 1st Int. Conf. on e-Science and Grid Computing, Melbourne, Australia, 5-8 December, pp. 361-368. Los Alamitos, CA: IEEE Computer Society. (doi:10.1109/E-SCIENCE.2005.19)
18. Greenstein, J. L., Hinch, R. & Winslow, R. L. 2006 Mechanisms of excitation-contraction coupling in an integrative model of the cardiac ventricular myocyte. Biophys. J. 90, 77-91. (doi:10.1529/biophysj.105.065169)
19. Hinch, R., Greenstein, J. L., Tanskanen, A. J., Xu, L. & Winslow, R. L. 2004 A simplified local control model of calcium-induced calcium release in cardiac ventricular myocytes. Biophys. J. 87, 3723-3736. (doi:10.1529/biophysj. 104.049973) (Pubitemid 39602882)
20. Keener, J. & Sneyd, J. 2001 Mathematical physiology. Berlin, Germany: Springer.
21. Kerckhoffs, R. C. P., Healy, S. N., Usyk, T. P. & McCulloch, A. D. 2006 Computational methods for cardiac electromechanics. Proc. IEEE 94, 769-783. (doi:10.1109/JPROC.2006. 871772) (Pubitemid 46444984)
22. 2+ in left ventricular myocyte sub-types from rabbits with heart failure. Cardiovasc. Res. 45, 397-409. (doi:10.1016/S0008-6363(99)00360-0)
23. Noble, D. 1960 Cardiac action and pacemaker potentials based on the Hodgkin-Huxley equations. Nature 188, 495-497. (doi:10.1038/188495b0)
24. Noble, D. 1962 A modification of the Hodgkin-Huxley equations applicable to Purkinje fibre action and pacemaker potentials. J. Physiol. 160, 317-352.
25. Noble, D., Varghese, A., Kohl, P. & Noble, P. 1998 Improved guinea-pig ventricular cell model incorporating a dyadic space, IKr and IKs, and length-and tension-dependent processes. Can. J. Cardiol. 14, 123-134.
26. Peachey, T. C., Diamond, N. T., Abramson, D. A., Sudholt, W., Michailova, A. & Amirriazi, S. 2008 Fractional factorial design for parameter sweep experiments using Nimrod/E. J. Sci. Prog. 16, 217-230.
27. Pitt-Francis, J. et al. 2009 Chaste: A test-driven approach to software development for biological modelling. Comput. Phys. Commun. 180, 2452-2471. (doi:10.1016/j.cpc.2009.07.019)
28. Plank, G., Prassl, A., Hofer, E. & Trayanova, N. A. 2008 Evaluating intramural virtual electrodes in the myocardial wedge preparation: Simulations of experimental conditions. Biophys. J. 94, 1904-1915. (doi:10.1529/biophysj. 107.121343)
29. Pueyo, E., Corrias, A., Gavaghan, D., Burrage, K. & Rodriguez, B. 2009 Role of stochastic IKs gating kinetics in arrhythmogenesis. Heart Rhythm 6 (Suppl., May), S296.
30. Rudy, Y. & Silva, J. R. 2006 Computational biology in the study of cardiac ion channels and cell electrophysiology. Q. Rev. Biophys. 39, 57-116. (doi:10.1017/S003358350 6004227)
31. 2+ dynamics into single cell ventricular models In Computational Science-ICCS 2008, Part I, Proc. 8th Int. Conf., Kraków, Poland, 23-25 June. Lecture Notes in Computer Science, no. 5101, pp. 66-75. Berlin, Germany: Springer. (doi:10.1007/978-3-540-69384-0-12)