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Items: 1 to 20 of 114

1.

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.

PMID:
19703920
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.

PMID:
19564239
3.

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.

4.

The CellML Model Repository.

Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF.

Bioinformatics. 2008 Sep 15;24(18):2122-3. doi: 10.1093/bioinformatics/btn390. Epub 2008 Jul 25.

PMID:
18658182
5.

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.

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.

Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A.

Bioinformatics. 2010 Apr 1;26(7):925-31. doi: 10.1093/bioinformatics/btq063. Epub 2010 Feb 16.

PMID:
20160009
8.

The Physiome Model Repository 2.

Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM.

Bioinformatics. 2011 Mar 1;27(5):743-4. doi: 10.1093/bioinformatics/btq723. Epub 2011 Jan 6.

PMID:
21216774
9.

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
10.

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
11.

Bioinformatics, multiscale modeling and the IUPS Physiome Project.

Hunter PJ, Crampin EJ, Nielsen PM.

Brief Bioinform. 2008 Jul;9(4):333-43. doi: 10.1093/bib/bbn024. Epub 2008 May 13.

PMID:
18477639
12.

CelOWS: an ontology based framework for the provision of semantic web services related to biological models.

Matos EE, Campos F, Braga R, Palazzi D.

J Biomed Inform. 2010 Feb;43(1):125-36. doi: 10.1016/j.jbi.2009.08.008. Epub 2009 Aug 18.

13.

Modelling heart beat initiation and propagation using the MML framework.

Chang D, Dokos S, Lovell NH.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:4495-8. doi: 10.1109/IEMBS.2009.5333683.

PMID:
19964371
14.

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
15.

The IUPS Physiome Project: a framework for computational physiology.

Hunter PJ.

Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):551-69. Review.

PMID:
15142761
16.

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.

17.

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
18.

Standards and ontologies in computational systems biology.

Sauro HM, Bergmann FT.

Essays Biochem. 2008;45:211-22. doi: 10.1042/BSE0450211. Review.

19.

CELLULAR OPEN RESOURCE (COR): current status and future directions.

Garny A, Noble D, Hunter PJ, Kohl P.

Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1885-905. doi: 10.1098/rsta.2008.0289.

20.

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.

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