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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum. Hucka M, et al. Among authors: nielsen pf. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808
The CellML Model Repository.
Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. Lloyd CM, et al. Among authors: nielsen pf. Bioinformatics. 2008 Sep 15;24(18):2122-3. doi: 10.1093/bioinformatics/btn390. Epub 2008 Jul 25. Bioinformatics. 2008. PMID: 18658182
The CellML 1.1 Specification.
Cuellar A, Hedley W, Nelson M, Lloyd C, Halstead M, Bullivant D, Nickerson D, Hunter P, Nielsen P. Cuellar A, et al. J Integr Bioinform. 2015 Sep 4;12(2):259. doi: 10.2390/biecoll-jib-2015-259. J Integr Bioinform. 2015. PMID: 26528557
Minimum information requested in the annotation of biochemical models (MIRIAM).
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Le Novère N, et al. Nat Biotechnol. 2005 Dec;23(12):1509-15. doi: 10.1038/nbt1156. Nat Biotechnol. 2005. PMID: 16333295
A strategy for integrative computational physiology.
Hunter P, Nielsen P. Hunter P, et al. Physiology (Bethesda). 2005 Oct;20:316-25. doi: 10.1152/physiol.00022.2005. Physiology (Bethesda). 2005. PMID: 16174871 Free article. Review.
Biophysical annotation and representation of CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF. Wimalaratne SM, et al. Among authors: nielsen pf. Bioinformatics. 2009 Sep 1;25(17):2263-70. doi: 10.1093/bioinformatics/btp391. Epub 2009 Jun 29. Bioinformatics. 2009. PMID: 19564239
A method for visualizing CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF. Wimalaratne SM, et al. Among authors: nielsen pf. Bioinformatics. 2009 Nov 15;25(22):3012-9. doi: 10.1093/bioinformatics/btp495. Epub 2009 Aug 24. Bioinformatics. 2009. PMID: 19703920
Minimum Information About a Simulation Experiment (MIASE).
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Waltemath D, et al. PLoS Comput Biol. 2011 Apr;7(4):e1001122. doi: 10.1371/journal.pcbi.1001122. Epub 2011 Apr 28. PLoS Comput Biol. 2011. PMID: 21552546 Free PMC article. No abstract available.
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. Miller AK, et al. Among authors: nielsen pf. BMC Bioinformatics. 2010 Apr 8;11:178. doi: 10.1186/1471-2105-11-178. BMC Bioinformatics. 2010. PMID: 20377909 Free PMC article.
116 results