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BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR. Shaikh B, et al. Among authors: smith lp. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
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.
209 results