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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. BMC Bioinformatics. 2014 Dec 14;15(1):369. doi: 10.1186/s12859-014-0369-z. BMC Bioinformatics. 2014. PMID: 25494900 Free PMC article.
Bifurcation discovery tool.
Chickarmane V, Paladugu SR, Bergmann F, Sauro HM. Chickarmane V, et al. Bioinformatics. 2005 Sep 15;21(18):3688-90. doi: 10.1093/bioinformatics/bti603. Epub 2005 Aug 4. Bioinformatics. 2005. PMID: 16081475
Supporting the SBML layout extension.
Deckard A, Bergmann FT, Sauro HM. Deckard A, et al. Among authors: bergmann ft. 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. Bioinformatics. 2008 Sep 1;24(17):1963-5. doi: 10.1093/bioinformatics/btn319. Epub 2008 Jun 25. Bioinformatics. 2008. PMID: 18579569 Free PMC article.
Antimony: a modular model definition language.
Smith LP, Bergmann FT, Chandran D, Sauro HM. Smith LP, et al. Among authors: bergmann ft. Bioinformatics. 2009 Sep 15;25(18):2452-4. doi: 10.1093/bioinformatics/btp401. Epub 2009 Jul 3. Bioinformatics. 2009. PMID: 19578039 Free PMC article.
TinkerCell: modular CAD tool for synthetic biology.
Chandran D, Bergmann FT, Sauro HM. Chandran D, et al. Among authors: bergmann ft. J Biol Eng. 2009 Oct 29;3:19. doi: 10.1186/1754-1611-3-19. J Biol Eng. 2009. PMID: 19874625 Free PMC article.
SBML2TikZ: supporting the SBML render extension in LaTeX.
Shen SY, Bergmann F, Sauro HM. Shen SY, et al. Bioinformatics. 2010 Nov 1;26(21):2794-5. doi: 10.1093/bioinformatics/btq512. Epub 2010 Sep 9. Bioinformatics. 2010. PMID: 20829443 Free PMC article.
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: bergmann ft. 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.
82 results