Belic JJ, Kumar A, Hellgren Kotaleski J (2017) Interactions in the Striatal Network with Different Oscillation Frequencies Artificial Neural Networks and Machine Learning -- ICANN 2017, Lintas, Alessandra and Rovetta, Stefano and Verschure, Paul F.M.J. and Villa, Alessandro E.P., ed. pp.129 [Journal]

Brette R, Goodman DF (2011) Vectorized algorithms for spiking neural network simulation. Neural Comput 23:1503-35 [Journal] [PubMed]

•	Vectorized algorithms for spiking neural network simulation (Brette and Goodman 2011) [Model]

Cattani A, Solinas S, Canuto C (2016) A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. Front Comput Neurosci 10:30 [Journal] [PubMed]

Chrysanthidis N, Fiebig F, Lansner A (2019) Introducing double bouquet cells into a modular cortical associative memory model Journal of Computational Neuroscience [Journal]

•	An electrophysiological model of GABAergic double bouquet cells (Chrysanthidis et al. 2019) [Model]

Crone JC, Vindiola MM, Yu AB, Boothe DL, Beeman D, Oie KS, Franaszczuk PJ (2019) Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator Frontiers in Neuroinformatics 13:69 [Journal]

•	ACnet23 primary auditory cortex model (Beeman et al 2019) [Model]
•	Large scale neocortical model for PGENESIS (Crone et al 2019) [Model]

Djurfeldt M (2012) The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models. Neuroinformatics 10:287-304 [Journal] [PubMed]

•	Connection-set Algebra (CSA) for the representation of connectivity in NN models (Djurfeldt 2012) [Model]

Fiebig F, Lansner A (2017) A Spiking Working Memory Model Based on Hebbian Short-Term Potentiation. J Neurosci 37:83-96 [Journal] [PubMed]

Gewaltig MO, Cannon R (2014) Current practice in software development for computational neuroscience and how to improve it. PLoS Comput Biol 10:e1003376 [Journal] [PubMed]

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]

Grein S, Stepniewski M, Reiter S, Knodel MM, Queisser G (2014) 1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time. Front Neuroinform 8:68 [Journal] [PubMed]

Hernández OE, Zurek EE (2013) Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON's programming language hoc. BMC Med Educ 13:70 [Journal] [PubMed]

•	Software for teaching the Hodgkin-Huxley model (Hernandez & Zurek 2013) (SENB written in NEURON hoc) [Model]

Hines M, Kumar S, Schürmann F (2011) Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Front Comput Neurosci 5:49 [Journal] [PubMed]

•	Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011) [Model]

Kobayashi R, Kurita S, Kurth A, Kitano K, Mizuseki K, Diesmann M, Richmond BJ, Shinomoto S (2019) Reconstructing neuronal circuitry from parallel spike trains. Nat Commun 10:4468 [Journal] [PubMed]

•	GLMCC validation neural network model (Kobayashi et al. 2019) [Model]

Kobayashi R, Tsubo Y, Shinomoto S (2009) Made-to-order spiking neuron model equipped with a multi-timescale adaptive threshold. Front Comput Neurosci 3:9 [Journal] [PubMed]

•	Multi-timescale adaptive threshold model (Kobayashi et al 2009) (NEURON) [Model]
•	Multi-timescale adaptive threshold model (Kobayashi et al 2009) [Model]

Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML (2016) Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput 28:2063-90 [Journal] [PubMed]

•	Parallelizing large networks in NEURON (Lytton et al. 2016) [Model]

Magalhães BRC, Sterling T, Hines M, Schürmann F (2019) Asynchronous Branch-Parallel Simulation of Detailed Neuron Models. Front Neuroinform 13:54 [Journal] [PubMed]

•	Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks (Magalhaes et al 2019) [Model]

Mäki-Marttunen T, Acimovic J, Ruohonen K, Linne ML (2013) Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework. PLoS One 8:e69373 [Journal] [PubMed]

•	Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013) [Model]

Manninen T, Hituri K, Kotaleski JH, Blackwell KT, Linne ML (2010) Postsynaptic signal transduction models for long-term potentiation and depression. Front Comput Neurosci 4:152 [Journal] [PubMed]

Martínez-Cañada P, Mobarhan MH, Halnes G, Fyhn M, Morillas C, Pelayo F, Einevoll GT (2018) Biophysical network modeling of the dLGN circuit: Effects of cortical feedback on spatial response properties of relay cells. PLoS Comput Biol 14:e1005930 [Journal] [PubMed]

•	Cortical feedback alters visual response properties of dLGN relay cells (Martínez-Cañada et al 2018) [Model]

Martínez-Cañada P, Morillas C, Pino B, Ros E, Pelayo F (2016) A Computational Framework for Realistic Retina Modeling. Int J Neural Syst 26:1650030 [Journal] [PubMed]

•	COREM: configurable retina simulator (Martínez-Cañada et al., 2016) [Model]

Mattioni M, Cohen U, Le Novère N (2012) Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 6:20 [Journal] [PubMed]

•	Neuronvisio: a gui with 3D capabilities for NEURON (Mattioni et al. 2012) [Model]

Mattioni M, Le Novère N (2013) Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PLoS One 8:e66811 [Journal] [PubMed]

•	Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013) [Model]

Morén J, Shibata T, Doya K (2013) The mechanism of saccade motor pattern generation investigated by a large-scale spiking neuron model of the superior colliculus. PLoS One 8:e57134 [Journal] [PubMed]

•	A spatial model of the intermediate superior colliculus (Moren et. al. 2013) [Model]

Richert M, Nageswaran JM, Dutt N, Krichmar JL (2011) An efficient simulation environment for modeling large-scale cortical processing. Front Neuroinform 5:19 [Journal] [PubMed]

•	Efficient simulation environment for modeling large-scale cortical processing (Richert et al. 2011) [Model]

Sadeh S, Rotter S (2015) Orientation selectivity in inhibition-dominated networks of spiking neurons: effect of single neuron properties and network dynamics. PLoS Comput Biol 11:e1004045 [Journal] [PubMed]

•	Orientation selectivity in inhibition-dominated recurrent networks (Sadeh and Rotter, 2015) [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]

Shimoura RO, Kamiji NL, Pena RFO, Cordeiro VL, Ceballos CC, Cecilia R, Roque AC (2018) [Re] The cell-type specific cortical microcircuit: relating structure and activity in a full-scale spiking network model The ReScience Journal [Journal]

•	A full-scale cortical microcircuit spiking network model (Shimoura et al 2018) [Model]

Singh N, Huyck C, Gandhi V, Jones A (2016) Neuron-Based Control Mechanisms for a Robotic Arm and Hand ICMRRS 2017: International Conference on Medical Robotics and Robotics for Surgery, Paris, France 3(2):660 [Journal]

•	Neuron-based control mechanisms for a robotic arm and hand (Singh et al 2017) [Model]

Solanka L, van Rossum MC, Nolan MF (2015) Noise promotes independent control of gamma oscillations and grid firing within recurrent attractor networks. Elife [Journal] [PubMed]

•	Noise promotes independent control of gamma oscillations and grid firing (Solanka et al 2015) [Model]

Tikidji-Hamburyan RA, Narayana V, Bozkus Z, El-Ghazawi TA (2017) Software for Brain Network Simulations: A Comparative Study Front. Neuroinform. [Journal]

•	Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017) [Model]

Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP (2014) Connection-type-specific biases make uniform random network models consistent with cortical recordings. J Neurophysiol 112:1801-14 [Journal] [PubMed]

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA, Cunningham MO, Kaiser M (2015) Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. Brain Struct Funct 220:2333-53 [Journal] [PubMed]

•	Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014) [Model]

Vannucci L, Falotico E, Laschi C (2017) Proprioceptive Feedback through a Neuromorphic Muscle Spindle Model. Front Neurosci 11:341 [Journal] [PubMed]

•	Neuromorphic muscle spindle model (Vannucci et al 2017) [Model]

Versace M, Ames H, Léveillé J, Fortenberry B, Gorchetchnikov A (2008) KInNeSS: a modular framework for computational neuroscience. Neuroinformatics 6:291-309 [Journal] [PubMed]

•	KInNeSS : a modular framework for computational neuroscience (Versace et al. 2008) [Model]

Yamazaki T, Ikeno H, Okumura Y, Satoh S, Kamiyama Y, Hirata Y, Inagaki K, Ishihara A, Kannon T, Usui S (2011) Simulation Platform: a cloud-based online simulation environment. Neural Netw 24:693-8 [Journal] [PubMed]