MicrocircuitDB: Citation Relationship

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Reference cited by multiple papers

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, SBML Forum (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-31 [PubMed]

References and models cited by this paper

References and models that cite this paper

Chen W, De Schutter E (2014) Python-based geometry preparation and simulation visualization toolkits for STEPS. Front Neuroinform 8:37 [Journal] [PubMed]

•	Python-based toolkits for STEPS (Chen and De Schutter 2014) [Model]

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6:e1000815 [Journal] [PubMed]

Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]

Mai Z, Liu H (2013) Random parameter sampling of a generic three-tier MAPK cascade model reveals major factors affecting its versatile dynamics PLoS ONE 8(1):e54441 [Journal] [PubMed]

•	A generic MAPK cascade model for random parameter sampling analysis (Mai and Liu 2013) [Model]

Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2019) BioModels-15 years of sharing computational models in life science. Nucleic Acids Res [Journal] [PubMed]

Manninen T, Havela R, Linne ML (2017) Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform. [Journal]

•	Ca2+ oscillations in single astrocytes (Lavrentovich and Hemkin 2008) (python) (Manninen et al 2017) [Model]
•	Glutamate-evoked Ca2+ oscillations in single astrocytes (Modified from Dupont et al. 2011) [Model]
•	Glutamate-evoked Ca2+ oscillations in single astrocytes (De Pitta et al. 2009) (Manninen et al 2017) [Model]
•	Reproducibility and comparability of models for astrocyte Ca2+ excitability (Manninen et al 2017) [Model]
•	Spontaneous calcium oscillations in single astrocytes (Riera et al. 2011) (Manninen et al 2017) [Model]

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in Computational Neuroscience Models and Simulations. IEEE Trans Biomed Eng 63:2021-35 [Journal] [PubMed]

McDougal RA, Hines ML, Lytton WW (2013) Reaction-diffusion in the NEURON simulator. Front Neuroinform 7:28 [Journal] [PubMed]

•	Reaction-diffusion in the NEURON simulator (McDougal et al 2013) [Model]

Niederer SA, Kerfoot E, Benson AP, Bernabeu MO, Bernus O, Bradley C, Cherry EM, Clayton R, Fenton FH, Garny A, Heidenreich E, Land S, Maleckar M, Pathmanathan P, Plank G, Rodríguez JF, Roy I, Sachse FB, Seemann G, Skavhaug O, Smith NP (2011) Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. Philos Trans A Math Phys Eng Sci 369:4331-51 [Journal] [PubMed]

Ray S, Bhalla US (2008) PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform 2:6 [Journal] [PubMed]

•	Moose/PyMOOSE: interoperable scripting in Python for MOOSE (Ray and Bhalla 2008) [Model]

Sherfey JS, Soplata AE, Ardid S, Roberts EA, Stanley DA, Pittman-Polletta BR, Kopell NJ (2018) DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. Front Neuroinform 12:10 [Journal] [PubMed]

•	DynaSim: a MATLAB toolbox for neural modeling and simulation (Sherfey et al 2018) [Model]

Waltemath D, Wolkenhauer O (2016) How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans Biomed Eng 63:1999-2006 [Journal] [PubMed]

Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM (2011) The Physiome Model Repository 2. Bioinformatics 27:743-4 [Journal] [PubMed]

(13 refs)