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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: sauro hm. BMC Bioinformatics. 2014 Dec 14;15(1):369. doi: 10.1186/s12859-014-0369-z. BMC Bioinformatics. 2014. PMID: 25494900 Free PMC article.
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: sauro hm. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808
Bifurcation discovery tool.
Chickarmane V, Paladugu SR, Bergmann F, Sauro HM. Chickarmane V, et al. Among authors: sauro hm. Bioinformatics. 2005 Sep 15;21(18):3688-90. doi: 10.1093/bioinformatics/bti603. Epub 2005 Aug 4. Bioinformatics. 2005. PMID: 16081475
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
Supporting the SBML layout extension.
Deckard A, Bergmann FT, Sauro HM. Deckard A, et al. Among authors: sauro hm. Bioinformatics. 2006 Dec 1;22(23):2966-7. doi: 10.1093/bioinformatics/btl520. Epub 2006 Oct 11. Bioinformatics. 2006. PMID: 17038346
Comparing simulation results of SBML capable simulators.
Bergmann FT, Sauro HM. Bergmann FT, et al. Among authors: sauro hm. Bioinformatics. 2008 Sep 1;24(17):1963-5. doi: 10.1093/bioinformatics/btn319. Epub 2008 Jun 25. Bioinformatics. 2008. PMID: 18579569 Free PMC article.
141 results