A physiome standards-based model publication paradigm

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

Volumn 367, Issue 1895, 2009, Pages 1823-1844

  Nickerson, David P ^a   Buist, Martin L ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Cellml; Mathematical model representation; Model publication; Physiome standards

Indexed keywords

COMPUTER SIMULATION; MARKUP LANGUAGES; PUBLISHING; STANDARDS; WEB BROWSERS;

BROADBAND INTERNET; CELLML; CELLULAR ELECTROPHYSIOLOGY; HUMAN-READABLE; MATHEMATICAL MODEL REPRESENTATION; NEW MODEL; PHYSIOME; PHYSIOME STANDARDS; STATE OF THE ART; SYSTEMS BIOLOGY MARKUP LANGUAGES; TECHNOLOGY-BASED;

MATHEMATICAL MODELS;

ARTICLE; AUDIOVISUAL EQUIPMENT; COMPUTER LANGUAGE; HUMAN; VALIDATION STUDY;

HUMANS; MODELS, ANATOMIC; PROGRAMMING LANGUAGES;

EID: 67149141595     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2008.0296     Document Type: Review

References (43)

1. Bankier, J.-G. and Perciali, I. 2008 The institutional repository rediscovered: what can a university do for open access publishing? Ser. Rev. 34, 21-26. (doi:10.1016/j.serrev. 2007.12.003)
2. Beard, D. A. 2005 A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation. PLoS Comput. Biol. 1, e36. (doi:10.1371/journal.pcbi.0010036)
3. Beard, D. A. et al. 2009 CellML metadata standards, associated tools and repositories. Phil. Trans. R. Soc. A 367, 1845-1867. (doi:10.1098/rsta.2008.0310)
4. Bergmann, F. T. and Sauro, H. M. 2008 Comparing simulation results of SBML capable simulators. Bioinformatics 24, 1963-1965. (doi:10.1093/bioinformatics/btn319)
5. Berners-Lee, T., Fielding, R. and Masinter, L. 2005 RFC 3986, uniform resource identifier (URI) : generic syntax. See http://www.ietf.org/rfc/rfc3986. txt.
6. Blackett, S. A., Bullivant, D. P., Nickerson, D. P. and Hunter, P. J. 2005 Multi-scale and multiphysics visualization. In SIGGRAPH '05: ACM SIGGRAPH 2005 Posters, p. 136. New York, NY: ACM Press. (doi:10.1145/ 1186954.1187109)
7. Christie, G. R., Nielsen, P. M. F., Blackett, S. A., Bradley, C. P. and Hunter, P. J. 2009 FieldML: concepts and implementation. Phil. Trans. R. Soc. A 367, 1869-1884. (doi:10.1098/rsta.2009. 0025)
8. Cooling, M. T., Hunter, P. and Crampin, E. J. 2008 Modelling biological modularity with Cell M.L. IET Syst. Biol. 2, 73-79. (doi:10.1049/iet-syb:20070020)
9. Corrias, A. and Buist, M. L. 2007 A quantitative model of gastric smooth muscle cellular activation. Ann. Biomed. Eng. 35, 1595-1607. (doi:10.1007/s10439-007-9324-8)
10. Corrias, A. and Buist, M. L. 2008 Quantitative cellular description of gastric slow wave activity. Am. J. Physiol. Gastrointest. Liver Physiol. 294, G989-G995. (doi:10.1152/ajpgi.00528.2007)
11. Cuellar, A. A., Lloyd, C. M., Nielson, P. F., Halstead, M. D. B., Bullivant, D. P., Nickerson, D. P. and Hunter, P. J. 2003 An overview of CellML 1.1, a biological model description language. Simulation 79, 740-747. (doi:10.1177/0037549703040939)
12. Demir, S. S. 2006 Interactive cell modeling web-resource, iCell, as a simulation-based teaching and learning tool to supplement electrophysiology education. Ann. Biomed. Eng. 34, 1077-1087. (doi:10.1007/s10439- 006-9138-0)
13. i overloaded cardiac myocytes: a simulation study. Biophys. J. 78, 2392-2404. (doi:10.1016/S0006-3495 (00) 76783-X)
14. Finney, A. and Hucka, M. 2003 Systems biology markup language: level 2 and beyond. Biochem. Soc. Trans. 31, 1472-1473. (doi:10.1042/BST0311472)
15. Garny, A., Nickerson, D. P., Cooper, J., Santos, R. W. D., Miller, A. K., McKeever, S., Nielsen, P. M. F. and Hunter, P. J. 2008 CellML and associated tools and techniques. Phil. Trans. R. Soc. A 366, 3017-3043. (doi:10.1098/rsta.2008.0094)
16. Hines, M. L., Morse, T., Migliore, M., Carnevale, N. T. and Shepherd, G. M. 2004 ModelDB: a database to support computational neuroscience. J. Comput. Neuro Sci. 17, 7-11. (doi:10.1023 /B:JCNS.0000023869.22017.2e)
17. Hucka, M. et al. 2003 The systems biology markup language (SBML) : a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093 /bioinformatics/btg015)
18. Jones, R. 2007 Giving birth to next generation repositories. Int. J. Inform. Manage. 27, 154-158. (doi:10.1016/j.ijinfomgt.2007.02.004)
19. Le Novère, N. et al. 2005 Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509-1515. (doi:10.1038/nbt1156)
20. 2+ and electrical alternans in cardiac myocytes: role of CAMKII and repolarizing currents. Am. J. Physiol. Heart Circ. Physiol. 292, H2854-H2866. (doi:10.1152/ajpheart.01347.2006)
21. Lloyd, C. M., Lawson, J. R., Hunter, P. J. and Nielsen, P. F. 2008 The CellML model repository. Bioinformatics 24, 2122-2123. (doi:10.1093/bioinformatics/btn390)
22. Loew, L. M. and 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)
23. Luo, C. H. and Rudy, Y. 1991 A model of the ventricular cardiac action potential. Depolarization, repolarization, and their interaction. Circ. Res. 68, 1501-1526.
24. Luo, C. H. and Rudy, Y. 1994 A dynamic model of the cardiac ventricular action potential. I. Simulations of ionic currents and concentration changes. Circ. Res. 74, 1071-1096.
25. Migliore, M., Morse, T. M., Davison, A. P., Marenco, L., Shepherd, G. M. and Hines, M. L. 2003 ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics 1, 135-139. (doi:10.1385/NI:1:1:135)
26. Nickerson, D. and Buist, M. 2008a Interactive reference descriptions of cellular electrophysiology models. In Engineering in Medicine and Biology Society, 2008. EMBS 2008. 30th Annual Int. Conf. of the IEEE, pp. 2427-2430.
27. Nickerson, D. and Buist, M. 2008b Practical application of CellML 1.1: the integration of new mechanisms into a human ventricular myocyte model. Prog. Biophys. Mol. Biol. 98, 38-51. (doi:10.1016/j.pbiomolbio. 2008.05.006)
28. Nickerson, D. P. and Hunter, P. J. 2006 The noble cardiac ventricular electrophysiology models in Cell M.L. Prog. Biophys. Mol. Biol. 90, 346-359. (doi:10.1016/j.pbiomolbio.2005.05.007)
29. Nickerson, D. P., Nash, M. P., Nielsen, P. F., Smith, N. P. and Hunter, P. J. 2006 Computational multiscale modeling in the IUPS physiome project: modeling cardiac electromechanics. IBM J. Res. Dev. 50, 617-630. (doi:10.1147/rd.506.0617)
30. Nickerson, D. P., Corrias, A. and Buist, M. L. 2008 Reference descriptions of cellular electrophysiology models. Bioinformatics 24, 1112-1114. (doi:10.1093/bioinformatics/btn080)
31. Niederer, S. A., Hunter, P. J. and Smith, N. P. 2006 A quantitative analysis of cardiac myocyte relaxation: a simulation study. Biophys. J. 90, 1697-1722. (doi:10.1529/biophysj.105.069534)
32. Puglisi, J. L. and Bers, D. M. 2001 LabHEART: an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport. Am. J. Physiol. Cell Physiol. 281, C2049-C2060.
33. Sachse, F. B., Moreno, A. P. and Abildskov, J. A. 2008 Electrophysiological modeling of fibroblasts and their interaction with myocytes. Ann. Biomed. Eng. 36, 41-56. (doi:10.1007/s10439-007- 9405-8)
34. 2+ exchanger knockout mice. J. Physiol. Sci. 56, 211-217. (doi:10.2170/physiolsci. RP005006)
35. Schilstra, M. J., Li, L., Matthews, J., Finney, A., Hucka, M. and Le Novère, N. 2006 CellML2SBML: conversion of CellML into SBML. Bioinformatics 22, 1018-1020. (doi:10.1093/bioinformatics /bt1047)
36. Schmid, H., Nash, M. P., Young, A. A., Röhrle, O. and Hunter, P. J. 2007 A computationally efficient optimization kernel for material parameter estimation procedures. J. Biomech. Eng. 129, 279-283. (doi:10.1115/1.2540860)
37. Seringhaus, M. R. and Gerstein, M. B. 2007 Publishing perishing? Towards tomorrow's information architecture. BMC Bioinform. 8, 17. (doi:10.1186/1471-2105-8-17)
38. Slepchenko, B. M., Schaff, J. C., Macara, I. and Loew, L. M. 2003 Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 13, 570-576. (doi:10.1016/j.tcb.2003.09.002)
39. Smith, N. P., Nickerson, D. P., Crampin, E. J. and Hunter, P. J. 2004 Multiscale computational modelling of the heart. Acta Numer. 13, 371-431.
40. - homeostasis and volume regulation of the cardiac cell. Phil. Trans. R. Soc. A 364, 1245-1265. (doi:10.1098/rsta.2006.1767)
41. Terkildsen, J. R., Niederer, S., Crampin, E. J., Hunter, P. and Smith, N. P. 2008 Using physiome standards to couple cellular functions for rat cardiac excitation-contraction. Exp. Physiol. 93, 919-929. (doi:10.1113/expphysiol.2007.041871)
42. Viswanathan, P. C., Shaw, R. M. and Rudy, Y. 1999 Effects of IKr and I Ks heterogeneity on action potential duration and its rate dependence: a simulation study. Circulation 99, 2466-2474.
43. + current in ventricular myocytes of the guinea pig type. Theoretical formulation and their role in repolarization. Circ. Res. 77, 140-152.