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SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Among authors: smith lp. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Antimony: a modular model definition language.
Smith LP, Bergmann FT, Chandran D, Sauro HM. Smith LP, et al. Bioinformatics. 2009 Sep 15;25(18):2452-4. doi: 10.1093/bioinformatics/btp401. Epub 2009 Jul 3. Bioinformatics. 2009. PMID: 19578039 Free PMC article.
SBML and CellML translation in antimony and JSim.
Smith LP, Butterworth E, Bassingthwaighte JB, Sauro HM. Smith LP, et al. Bioinformatics. 2014 Apr 1;30(7):903-7. doi: 10.1093/bioinformatics/btt641. Epub 2013 Nov 8. Bioinformatics. 2014. PMID: 24215024 Free PMC article.
A reappraisal of how to build modular, reusable models of biological systems.
Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. Neal ML, et al. Among authors: smith lp. PLoS Comput Biol. 2014 Oct 2;10(10):e1003849. doi: 10.1371/journal.pcbi.1003849. eCollection 2014 Oct. PLoS Comput Biol. 2014. PMID: 25275523 Free PMC article. No abstract available.
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
Choi K, Smith LP, Medley JK, Sauro HM. Choi K, et al. Among authors: smith lp. J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30. J Bioinform Comput Biol. 2016. PMID: 27774871 Free PMC article.
SBML Level 3 package: Groups, Version 1 Release 1.
Hucka M, Smith LP. Hucka M, et al. Among authors: smith lp. J Integr Bioinform. 2016 Dec 18;13(3):290. doi: 10.2390/biecoll-jib-2016-290. J Integr Bioinform. 2016. PMID: 28187406 Free PMC article.
209 results