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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: mcdougal r. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. Dura-Bernal S, et al. Elife. 2019 Apr 26;8:e44494. doi: 10.7554/eLife.44494. Elife. 2019. PMID: 31025934 Free PMC article.
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Gleeson P, et al. Among authors: mcdougal ra. Neuron. 2019 Aug 7;103(3):395-411.e5. doi: 10.1016/j.neuron.2019.05.019. Epub 2019 Jun 11. Neuron. 2019. PMID: 31201122 Free PMC article.
Water-tight membranes from neuronal morphology files.
McDougal RA, Hines ML, Lytton WW. McDougal RA, et al. J Neurosci Methods. 2013 Nov 15;220(2):167-78. doi: 10.1016/j.jneumeth.2013.09.011. Epub 2013 Sep 30. J Neurosci Methods. 2013. PMID: 24091136 Free PMC article.
Reaction-diffusion in the NEURON simulator.
McDougal RA, Hines ML, Lytton WW. McDougal RA, et al. Front Neuroinform. 2013 Nov 15;7:28. doi: 10.3389/fninf.2013.00028. eCollection 2013. Front Neuroinform. 2013. PMID: 24298253 Free PMC article.
3D-printer visualization of neuron models.
McDougal RA, Shepherd GM. McDougal RA, et al. Front Neuroinform. 2015 Jun 30;9:18. doi: 10.3389/fninf.2015.00018. eCollection 2015. Front Neuroinform. 2015. PMID: 26175684 Free PMC article.
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