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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: schaff jc. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
Virtual Cell modelling and simulation software environment.
Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, Lakshminarayana A, Gao F, Li Y, Loew LM. Moraru II, et al. Among authors: schaff jc. IET Syst Biol. 2008 Sep;2(5):352-62. doi: 10.1049/iet-syb:20080102. IET Syst Biol. 2008. PMID: 19045830 Free PMC article.
Kinetic Modeling using BioPAX ontology.
Ruebenacker O, Moraru II, Schaff JC, Blinov ML. Ruebenacker O, et al. Among authors: schaff jc. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2007 Nov 2;2007:339-348. doi: 10.1109/BIBM.2007.55. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2007. PMID: 20862270 Free PMC article.
Integrating BioPAX pathway knowledge with SBML models.
Ruebenacker O, Moraru II, Schaff JC, Blinov ML. Ruebenacker O, et al. Among authors: schaff jc. IET Syst Biol. 2009 Sep;3(5):317-28. doi: 10.1049/iet-syb.2009.0007. IET Syst Biol. 2009. PMID: 21028923 Free article.
Spatial modeling of cell signaling networks.
Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM. Cowan AE, et al. Among authors: schaff jc. Methods Cell Biol. 2012;110:195-221. doi: 10.1016/B978-0-12-388403-9.00008-4. Methods Cell Biol. 2012. PMID: 22482950 Free PMC article.
Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Blinov ML, Schaff JC, Ruebenacker O, Wei X, Vasilescu D, Gao F, Morgan F, Ye L, Lakshminarayana A, Moraru II, Loew LM. Blinov ML, et al. Among authors: schaff jc. Bioinformatics. 2014 Jan 15;30(2):292-4. doi: 10.1093/bioinformatics/btt660. Epub 2013 Nov 22. Bioinformatics. 2014. PMID: 24273241 Free PMC article.
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