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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. Among authors: miller ak. 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.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. Bergmann FT, et al. Among authors: miller ak. BMC Bioinformatics. 2014 Dec 14;15(1):369. doi: 10.1186/s12859-014-0369-z. BMC Bioinformatics. 2014. PMID: 25494900 Free PMC article.
CellML and associated tools and techniques.
Garny A, Nickerson DP, Cooper J, Weber dos Santos R, Miller AK, McKeever S, Nielsen PM, Hunter PJ. Garny A, et al. Among authors: miller ak. Philos Trans A Math Phys Eng Sci. 2008 Sep 13;366(1878):3017-43. doi: 10.1098/rsta.2008.0094. Philos Trans A Math Phys Eng Sci. 2008. PMID: 18579471 Review.
A Bayesian search for transcriptional motifs.
Miller AK, Print CG, Nielsen PM, Crampin EJ. Miller AK, et al. PLoS One. 2010 Nov 18;5(11):e13897. doi: 10.1371/journal.pone.0013897. PLoS One. 2010. PMID: 21124986 Free PMC article.
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. Beard DA, et al. Philos Trans A Math Phys Eng Sci. 2009 May 28;367(1895):1845-67. doi: 10.1098/rsta.2008.0310. Philos Trans A Math Phys Eng Sci. 2009. PMID: 19380315 Free PMC article.
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. Yu T, et al. Among authors: miller ak. Bioinformatics. 2011 Mar 1;27(5):743-4. doi: 10.1093/bioinformatics/btq723. Epub 2011 Jan 6. Bioinformatics. 2011. PMID: 21216774
259 results