CellML and associated tools and techniques

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

Volumn 366, Issue 1878, 2008, Pages 3017-3043

  Garny, Alan ^a   Nickerson, David P ^b   Cooper, Jonathan ^a   Santos, Rodrigo Weber Dos ^c   Miller, Andrew K ^d   McKeever, Steve ^a   Nielsen, Poul M F ^d   Hunter, Peter J ^d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c FEDERAL UNIVERSITY OF JUIZ DE FORA   (Brazil)

^d UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

API; CellML; IUPS Physiome Project; Mark up language; Modelling environment; XML

Indexed keywords

CHLORINE COMPOUNDS; COMPUTER SYSTEMS; LINGUISTICS; QUERY LANGUAGES; SPECIFICATIONS;

API; APPLICATION PROGRAM INTERFACE; BIOLOGICAL STRUCTURES; CELLML; CODE GENERATORS; COMPUTER MODELLING; FUTURE DIRECTIONS; HUMAN BODIES; INTERNATIONAL UNION OF PHYSIOLOGICAL SCIENCES; IUPS PHYSIOME PROJECT; MARK-UP LANGUAGE; MARK-UP LANGUAGES; MODELLING ENVIRONMENT; MULTI SCALING; MULTI-PHYSICS; ONLINE REPOSITORIES; SIMULATION ENVIRONMENTS; TOOLS AND TECHNIQUES; XML;

PHYSIOLOGICAL MODELS;

BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER SIMULATION; HUMAN; ONLINE SYSTEM; PHYSIOLOGY; REVIEW;

COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; ONLINE SYSTEMS; PHYSIOLOGY; PROGRAMMING LANGUAGES;

EID: 48349089965     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2008.0094     Document Type: Review

References (23)

1. Barbosa, C., Santos, R., Amorim, R., Ciuffo, L., Manfroi, F., Oliveira, R. & Campos, F. 2006 A transformation tool for ODE based models. Lecture Notes in Computer Science, 3991, pp. 69-75.
2. Bondarenko, V. E., Szigeti, G. P., Bett, G. C., Kim, S. J. & Rasmusson, R. L. 2004 Computer model of action potential of mouse ventricular myocytes. Am. J. Physiol. Heart Circ. Physiol. 287, 1378-1403. (doi:10.1152/ajpheart.00185.2003)
3. Cooper, J. & McKeever, S. 2007 Experience report: a Haskell interpreter for CellML. In: ICFP '07: Proc. 12th ACM SIGPLAN International Conf. on Funct. Programming, pp.247-250. New York, NY: ACM Press.
4. Cooper, J. & McKeever, S. 2008 A model-driven approach to automatic conversion of physical units. Softw. Pract. Exp. 38, 337-359. (doi:10.1002/spe.828)
5. Cooper, J., McKeever, S. & Garny, A. 2006 On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations. In: PEPM '06: Proc. 2006 ACM SIGPLAN Symp. on Partial Evaluation and Semantics-based Program Manipulation, pp. 12-20. New York, NY: ACM Press.
6. Courtemanche, M., Ramirez, R. J. &Nattel, S. 1998 Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model. Am. J. Physiol. 275, H301-H321.
7. Cuellar, A., Lloyd, M., Nielsen, P., Bullivant, D., Nickerson, D. & Hunter, P. 2003 An overview of CellML 1.1, a biological model description language. Simulation 79, 740-747. (doi:10.1177/ 0037549703040939)
8. Dexter, F., Saidel, G. M., Levy, M. N. & Rudy, Y. 1989 Mathematical model of dependence of heart rate on tissue concentration of acetylcholine. Am. J. Physiol. Heart Circ. Physiol. 256, H520-H526.
9. i overloaded cardiac myocytes: a simulation study. Biophys. J. 78, 2392-2404.
10. Garny, A., Kohl, P. & Noble, D. 2003a Cellular Open Resource (COR): a public CellML based environment for modelling biological function. Int. J. Bif. Chaos 13, 3579-3590. (doi:10.1142/ S021812740300882X)
11. Garny, A., Kohl, P., Hunter, P. J., Boyett, M. R. & Noble, D. 2003b One-dimensional rabbit sinoatrial node models: benefits and limitations. J. Cardiovasc. Electrophysiol. 14, S121-S132. (doi:10.1046/j.1540.8167.90301.x)
12. Hindmarsh, A. C., Brown, P. N., Grant, K. E., Lee, S. L., Serban, R., Shumaker, D. E. & Woodward, C. S. 2005 SUNDIALS: suite of nonlinear and differential/algebraic equation solvers. ACM Trans. Math. Softw. 31, 363-396. (doi:10.1145/1089014.1089020)
13. Isbell, D. & Savage, D. 1999 Mars climate orbiter failure board releases report, numerous NASA actions underway in response. NASA Press Release, pp. 99-134.
14. Jones, N. D., Gomard, C. K. & Sestoft, P. 1993 Partial evaluation and automatic program generation. Englewood Cliffs, NJ: Prentice Hall.
15. Lloyd, C. M., Halstead, M. D. & Nielsen, P. F. 2004 CellML: its future, present and past. Prog. Biophys. Mol. Biol. 85, 433-450. (doi:10.1016/j.pbiomolbio.2004.01.004)
16. Loew, L. M. & Schaff, J. C. 2001 The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol. 19, 401-406. (doi:10.1016/S0167-7799(01)01740-1)
17. Luo, C. & Rudy, Y. 1991 A model of the ventricular cardiac action potential-depolarisation, repolarisation and their interaction. Circ. Res. 68, 1501-1526.
18. Nickerson, D. & Hunter, P. 2006 The Noble cardiac ventricular electrophysiology models in CellML. Prog. Biophys. Mol. Biol. 90, 346-359. (doi:10.1016/j.pbiomolbio.2005.05.007)
19. Nickerson, D. P., Corrias, A. & Buist, M. L. 2008 Reference descriptions of cellular electrophysiology models. Bioinformatics 24, 1112-1114. (doi:10.1093/bioinformatics/btn080)
20. Noble, D. 1962 A modification of the Hodgkin - Huxley equations applicable to Purkinje fibre action and pacemaker potentials. J. Physiol. 160, 317-352.
21. Noble, D., Varghese, A., Kohl, P. & Noble, P. 1998 Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes. Can. J. Cardiol. 14, 123-134.
22. Nygren, A., Fiset, C., Firek, L., Clark, J. W., Lindblad, D. S., Clark, R. B. & Giles, W. R. 1998 Mathematical model of an adult human atrial cell: the role of K+ currents in repolarization. Circ. Res. 82, 63-81.
23. ten Tusscher, K. H. W. J. & Panfilov, A. V. 2006 Cell model for efficient simulation of wave propagation in human ventricular tissue under normal and pathological conditions. Phys. Med. Biol. 51, 6141-6156. (doi:10.1088/0031-9155/51/23/014)