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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: myers cj. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
The synthetic biology open language.
Myers C, Clancy K, Misirli G, Oberortner E, Pocock M, Quinn J, Roehner N, Sauro HM. Myers C, et al. Methods Mol Biol. 2015;1244:323-36. doi: 10.1007/978-1-4939-1878-2_16. Methods Mol Biol. 2015. PMID: 25487105
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.
Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N. Hucka M, et al. Among authors: myers cj. Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Front Bioeng Biotechnol. 2015. PMID: 25759811 Free PMC article. Review.
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.
Smith LP, Hucka M, Hoops S, Finney A, Ginkel M, Myers CJ, Moraru I, Liebermeister W. Smith LP, et al. Among authors: myers cj. J Integr Bioinform. 2015 Sep 4;12(2):268. doi: 10.2390/biecoll-jib-2015-268. J Integr Bioinform. 2015. PMID: 26528566 Free PMC article.
Toward Community Standards and Software for Whole-Cell Modeling.
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Waltemath D, et al. Among authors: myers cj. IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10. IEEE Trans Biomed Eng. 2016. PMID: 27305665 Free PMC article.
Synthetic Biology Open Language (SBOL) Version 2.2.0.
Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A. Cox RS, et al. J Integr Bioinform. 2018 Apr 2;15(1):20180001. doi: 10.1515/jib-2018-0001. J Integr Bioinform. 2018. PMID: 29605823 Free PMC article.
Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. Waltemath D, et al. Among authors: myers cj. Stand Genomic Sci. 2018 Aug 9;13:17. doi: 10.1186/s40793-018-0320-4. eCollection 2018. Stand Genomic Sci. 2018. PMID: 30117501 Free PMC article.
139 results