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Items: 1 to 20 of 125

1.

Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts.

Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.

Exp Physiol. 2009 May;94(5):472-85. doi: 10.1113/expphysiol.2008.045161. Epub 2009 Jan 16.

2.

Biophysical annotation and representation of CellML models.

Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF.

Bioinformatics. 2009 Sep 1;25(17):2263-70. doi: 10.1093/bioinformatics/btp391. Epub 2009 Jun 29.

3.

A method for visualizing CellML models.

Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.

Bioinformatics. 2009 Nov 15;25(22):3012-9. doi: 10.1093/bioinformatics/btp495. Epub 2009 Aug 24.

4.

Modelling biological modularity with CellML.

Cooling MT, Hunter P, Crampin EJ.

IET Syst Biol. 2008 Mar;2(2):73-9. doi: 10.1049/iet-syb:20070020.

PMID:
18397118
5.

CellML: its future, present and past.

Lloyd CM, Halstead MD, Nielsen PF.

Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):433-50. Review.

PMID:
15142756
6.

CellML and associated tools and techniques.

Garny A, Nickerson DP, Cooper J, Weber dos Santos R, Miller AK, McKeever S, Nielsen PM, Hunter PJ.

Philos Trans A Math Phys Eng Sci. 2008 Sep 13;366(1878):3017-43. doi: 10.1098/rsta.2008.0094. Review.

7.

OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.

Bradley C, Bowery A, Britten R, Budelmann V, Camara O, Christie R, Cookson A, Frangi AF, Gamage TB, Heidlauf T, Krittian S, Ladd D, Little C, Mithraratne K, Nash M, Nickerson D, Nielsen P, Nordbø O, Omholt S, Pashaei A, Paterson D, Rajagopal V, Reeve A, Röhrle O, Safaei S, Sebastián R, Steghöfer M, Wu T, Yu T, Zhang H, Hunter P.

Prog Biophys Mol Biol. 2011 Oct;107(1):32-47. doi: 10.1016/j.pbiomolbio.2011.06.015. Epub 2011 Jul 7.

PMID:
21762717
8.

Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model.

Nickerson D, Buist M.

Prog Biophys Mol Biol. 2008 Sep;98(1):38-51. doi: 10.1016/j.pbiomolbio.2008.05.006. Epub 2008 Jun 23. Review.

PMID:
18606438
9.

CellML metadata standards, associated tools and repositories.

Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T.

Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1845-67. doi: 10.1098/rsta.2008.0310.

10.

Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction.

Terkildsen JR, Niederer S, Crampin EJ, Hunter P, Smith NP.

Exp Physiol. 2008 Jul;93(7):919-29. doi: 10.1113/expphysiol.2007.041871. Epub 2008 Mar 14.

11.

Specifications of insilicoML 1.0: a multilevel biophysical model description language.

Asai Y, Suzuki Y, Kido Y, Oka H, Heien E, Nakanishi M, Urai T, Hagihara K, Kurachi Y, Nomura T.

J Physiol Sci. 2008 Dec;58(7):447-58. doi: 10.2170/physiolsci.RP013308. Epub 2008 Nov 6.

PMID:
18983726
12.

SysBioMed report: advancing systems biology for medical applications.

Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I.

IET Syst Biol. 2009 May;3(3):131-6. doi: 10.1049/iet-syb.2009.0005.

PMID:
19449974
13.

An overview of the CellML API and its implementation.

Miller AK, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, Nielsen PF.

BMC Bioinformatics. 2010 Apr 8;11:178. doi: 10.1186/1471-2105-11-178.

14.

Declarative representation of uncertainty in mathematical models.

Miller AK, Britten RD, Nielsen PM.

PLoS One. 2012;7(7):e39721. doi: 10.1371/journal.pone.0039721. Epub 2012 Jul 3.

15.

A platform for in silico modeling of physiological systems II. CellML compatibility and other extended capabilities.

Suzuki Y, Asai Y, Kawazu T, Nakanishi M, Taniguchi Y, Heien E, Hagihara K, Kurachi Y, Nomura T.

Conf Proc IEEE Eng Med Biol Soc. 2008;2008:573-6. doi: 10.1109/IEMBS.2008.4649217.

PMID:
19162720
16.

Cell system ontology: representation for modeling, visualizing, and simulating biological pathways.

Jeong E, Nagasaki M, Saito A, Miyano S.

In Silico Biol. 2007;7(6):623-38.

PMID:
18467775
17.

Tools for Modelling Biological Systems with CellML.

[No authors listed]

Conf Proc IEEE Eng Med Biol Soc. 2005;1:801-4.

PMID:
17282305
18.

Toward a curated CellML model repository.

Nickerson D, Stevens C, Halstead M, Hunter P, Nielsen P.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:4237-40.

PMID:
17947072
19.

Revision history aware repositories of computational models of biological systems.

Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PM.

BMC Bioinformatics. 2011 Jan 14;12:22. doi: 10.1186/1471-2105-12-22.

20.

ALC: automated reduction of rule-based models.

Koschorreck M, Gilles ED.

BMC Syst Biol. 2008 Oct 31;2:91. doi: 10.1186/1752-0509-2-91.

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