Considerations for the use of cellular electrophysiology models within cardiac tissue simulations

Progress in Biophysics and Molecular Biology

Volumn 107, Issue 1, 2011, Pages 74-80

  Cooper, Jonathan ^a   Corrias, Alberto ^a,b   Gavaghan, David ^a   Noble, Denis ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Cardiac electrophysiology; CellML; Chaste; Model interfaces

Indexed keywords

BIOLOGICAL MODEL; COMPUTER PROGRAM; CYTOLOGY; ELECTROPHYSIOLOGY; HEART; HEART MUSCLE; PHYSIOLOGY; REVIEW;

ELECTROPHYSIOLOGICAL PROCESSES; HEART; MODELS, BIOLOGICAL; MYOCARDIUM; SOFTWARE;

EID: 80053591347     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2011.06.002     Document Type: Review

References (30)

1. Beard D.A., Britten R., Cooling M.T., Garny A., Halstead M.D.B., Hunter P.J., Lawson J., Lloyd C.M., Marsh J., Miller A., Nickerson D.P., Nielsen P.M.F., Nomura T., Subramanium S., Wimalaratne S.M., Yu T. CellML metadata standards, associated tools and repositories. Physical and Engineering Sciences 2009, 367:1845-1867.
2. Bradley C., Bowery A., Britten R., Budelmann V., Camara O. OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project. Progress in Biophysics and Molecular Biology, 2011, 107:32-47.
3. Christie G.R., Nielsen P.M.F., Blackett S.A., Bradley C.P., Hunter P.J. FieldML: concepts and implementation. Philosophical Transactions of the Royal Society A 2009, 367:1869-1884.
4. Clayton R.H., Bernus O., Cherry E.M., Dierckx H., Fenton F.H., Mirabella L., Panfilov A.V., Sachse F.B., Seemann G., Zhang H. Models of cardiac tissue electrophysiology: progress, challenges and open questions. Progress in Biophysics and Molecular Biology 2010, 104:22-48.
5. Cooper, J., 2009. Automatic Validation and Optimisation of Biological Models. Ph.D. thesis, University of Oxford.
6. Cooper J., McKeever S. A model-driven approach to automatic conversion of physical units. Software Practice and Experience 2008, 38:337-359.
7. Cooper J., Mirams G., Niederer S. High throughput functional curation of cellular models. Progress in Biophysics and Molecular Biology 2011, 107:11-20.
8. DiFrancesco D., Noble D. A model of cardiac electrical activity incorporating ionic pumps and concentration changes. Philosophical Transactions of the Royal Society B 1985, 307:353-398.
9. Dokos S., Celler B., Lovell N. Ion currents underlying sinoatrial node pacemaker activity: a new single cell mathematical model. Journal of Theoretical Biology 1996, 181:245-272.
10. Garny A., Nickerson D., Cooper J., dos Santos R.W., McKeever S., Nielsen P., Hunter P. CellML and associated tools and techniques. Philosophical Transactions of the Royal Society A 2008, 366:3017-3043.
11. Hund T.J., Rudy Y. Rate dependence and regulation of action potential and calcium transient in a canine cardiac ventricular cell model. Circulation 2004, 110:3168-3174.
12. 2+ dynamics: the roles of ryanodine receptor adaptation and sarcoplasmic reticulum load. Biophysical Journal 1998, 74:1149-1168.
13. Keener J., Sneyd J. Mathematical Physiology. Interdisciplinary Applied Mathematics 1998, vol. 8. Springer.
14. Lloyd C.M., Halstead M.D., Nielsen P.F. CellML: its future, present and past. Progress in Biophysics and Molecular Biology 2004, 85:433-450.
15. Lloyd C.M., Lawson J.R., Hunter P.J., Nielsen P.F. The CellML model repository. Bioinformatics 2008, 24:2122-2123.
16. Luo C., Rudy Y. A model of the ventricular cardiac action potential: depolarization, repolarization, and their interaction. Circulation Research 1991, 68:1501-1526.
17. Mahajan A., Shiferaw Y., Sato D., Baher A., Olcese R., Xie L.H., Yang M.J., Chen P.S., Restrepo J.G., Karma A., Garfinkel A., Qu Z., Weiss J.N. A rabbit ventricular action potential model replicating cardiac dynamics at rapid heart rates. Biophysical Journal 2008, 94:392-410.
18. Matsuoka S., Sarai N., Kuratomi S., Ono K., Noma A. Role of individual ionic current systems in ventricular cells hypothesized by a model study. The Japanese Journal of Physiology 2003, 53:105-123.
19. Niederer, S.A., Kerfoot, E., Benson, A., Bernabeu, M.O., Bernus, O., Bradley, C., Cherry, E.M., Clayton, R., Fenton, F.H., Garny, A., Heidenreich, E., Land, S., Maleckar, M., Pathmanathan, P., Plank, G., Rodríguez, J.F., Roy, I., Sachse, F.B., Seemann, G., Skavhaug, O., Smith, N.P., Verification of cardiac tissue electrophysiology simulators using an n-version benchmark. Philosophical Transactions of the Royal Society A, in press.
20. Noble D., Varghese A., Kohl P., Noble P. Improved guinea-pig ventricular cell model incorporating a diadic space, iKr and iKs, length- and tension-dependent processes. Canadian Journal of Cardiology 1998, 14:123-134.
21. Pathmanathan P., Bernabeu M.O., Bordas R., Cooper J., Garny A., Pitt-Francis J.M., Whiteley J.P., Gavaghan D.J. A numerical guide to the solution of the bidomain equations of cardiac electrophysiology. Progress in Biophysics and Molecular Biology 2010, 102:136-155.
22. Pathmanathan P., Chapman S.J., Gavaghan D.J., Whiteley J.P. Cardiac electromechanics: the effect of contraction model on the mathematical problem and accuracy of the numerical scheme. The Quarterly Journal of Mechanics and Applied Mathematics 2010, 63:375-399.
23. Pathmanathan P., Mirams G., Southern J., Whiteley J. The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations. International Journal for Numerical Methods in Biomedical Engineering 2011.
24. Pitt-Francis J., Pathmanathan P., Bernabeu M.O., Bordas R., Cooper J., Fletcher A.G., Mirams G.R., Murray P., Osbourne J.M., Walter A., Chapman J., Garny A., van Leeuwen I.M.M., Maini P.K., Rodriguez B., Waters S.L., Whiteley J.P., Byrne H.M., Gavaghan D.J. Chaste: a test-driven approach to software development for biological modelling. Computer Physics Communications 2009, 180:2452-2471.
25. Priebe L., Beuckelmann D.J. Simulation study of cellular electric properties in heart failure. Circulation Research 1998, 82:1206-1223.
26. Quinn T., Antzelevitch C., Bollensdorf C., Bub G., RAB B., Chen P. Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. Progress in Biophysics and Molecular Biology 2011, 107:4-10.
27. Sampson K.J., Iyer V., Marks A.R., Kass R.S. A computational model of Purkinje fibre single cell electrophysiology: implications for the long QT syndrome. The Journal of Physiology 2010, 588:2643-2655.
28. Stewart P., Aslanidi O.V., Noble D., Noble P.J., Boyett M.R., Zhang H. Mathematical models of the electrical action potential of Purkinje fibre cells. Philosophical Transactions of the Royal Society A 2009, 367:2225-2255.
29. Terkildsen J.R., Niederer S., Crampin E.J., Hunter P., Smith N.P. Using physiome standards to couple cellular functions for rat cardiac excitation-contraction. Experimental Physiology 2008, 93:919-929.
30. Viswanathan P.C., Shaw R.M., Rudy Y. Effects of IKr and IKs heterogeneity on action potential duration and its rate dependence: a simulation study. Circulation 1999, 99:2466-2474.