Circuits that contain the Modeling Application : NEURON ()

(NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. It evolved from a long collaboration between Michael Hines and John W. Moore at the Department of Neurobiology, Duke University. Their express goal was to create a tool designed specifically for solving the equations that describe nerve cells.) Re-display model names with descriptions

	Models
1.	2D model of olfactory bulb gamma oscillations (Li and Cleland 2017)
2.	3D model of the olfactory bulb (Migliore et al. 2014)
3.	3D olfactory bulb: operators (Migliore et al, 2015)
4.	A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)
5.	A cerebellar model of phase-locked tACS for essential tremor (Schreglmann et al., 2021)
6.	A cortico-cerebello-thalamo-cortical loop model under essential tremor (Zhang & Santaniello 2019)
7.	A focal seizure model with ion concentration changes (Gentiletti et al., 2022)
8.	A Model Circuit of Thalamocortical Convergence (Behuret et al. 2013)
9.	A model of ASIC1a and synaptic cleft pH modulating wind-up in wide dynamic range neurons (Delrocq)
10.	A network model of the vertebrate retina (Publio et al. 2009)
11.	A network of AOB mitral cells that produces infra-slow bursting (Zylbertal et al. 2017)
12.	A single column thalamocortical network model (Traub et al 2005)
13.	A two networks model of connectivity-dependent oscillatory activity (Avella OJ et al. 2014)
14.	A two-layer biophysical olfactory bulb model of cholinergic neuromodulation (Li and Cleland 2013)
15.	Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)
16.	Basal ganglia network model of subthalamic deep brain stimulation (Hahn and McIntyre 2010)
17.	Biophysically Realistic Network Model of the Wild-Type and Degenerate Retina (Ly et al 2022)
18.	Biophysically realistic neural modeling of the MEG mu rhythm (Jones et al. 2009)
19.	Broadening of activity with flow across neural structures (Lytton et al. 2008)
20.	Bursting respiratory net: clustered architecture gives large phase diff`s (Fietkiewicz et al 2011)
21.	Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016)
22.	CA1 network model for place cell dynamics (Turi et al 2019)
23.	CA1 network model: interneuron contributions to epileptic deficits (Shuman et al 2020)
24.	CA1 pyr cell: Inhibitory modulation of spatial selectivity+phase precession (Grienberger et al 2017)
25.	CA1 pyramidal cell: reconstructed axonal arbor and failures at weak gap junctions (Vladimirov 2011)
26.	CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)
27.	Cell splitting in neural networks extends strong scaling (Hines et al. 2008)
28.	Cerebellar cortex oscil. robustness from Golgi cell gap jncs (Simoes de Souza and De Schutter 2011)
29.	Changes of ionic concentrations during seizure transitions (Gentiletti et al. 2016)
30.	Classic model of the Tritonia Swim CPG (Getting, 1989)
31.	Competition for AP initiation sites in a circuit controlling simple learning (Cruz et al. 2007)
32.	Computational analysis of NN activity and spatial reach of sharp wave-ripples (Canakci et al 2017)
33.	Computational Surgery (Lytton et al. 2011)
34.	Computer model of clonazepam's effect in thalamic slice (Lytton 1997)
35.	Convergence regulates synchronization-dependent AP transfer in feedforward NNs (Sailamul et al 2017)
36.	Cortical Basal Ganglia Network Model during Closed-loop DBS (Fleming et al 2020)
37.	Cortical feedback alters visual response properties of dLGN relay cells (Martínez-Cañada et al 2018)
38.	Cortical model with reinforcement learning drives realistic virtual arm (Dura-Bernal et al 2015)
39.	Current Dipole in Laminar Neocortex (Lee et al. 2013)
40.	Deconstruction of cortical evoked potentials generated by subthalamic DBS (Kumaravelu et al 2018)
41.	Decorrelation in the developing visual thalamus (Tikidji-Hamburyan et al, accepted)
42.	Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007)
43.	Dentate Gyrus Feed-forward inhibition (Ferrante et al. 2009)
44.	Dentate gyrus network model (Santhakumar et al 2005)
45.	Dentate gyrus network model (Tejada et al 2014)
46.	Dentate gyrus network model pattern separation and granule cell scaling in epilepsy (Yim et al 2015)
47.	Distal inhibitory control of sensory-evoked excitation (Egger, Schmitt et al. 2015)
48.	Distance-dependent inhibition in the hippocampus (Strüber et al. 2017)
49.	Duration-tuned neurons from the inferior colliculus of vertebrates (Aubie et al. 2012)
50.	Effects of increasing CREB on storage and recall processes in a CA1 network (Bianchi et al. 2014)
51.	Effects of spinal cord stimulation on WDR dorsal horn network (Zhang et al 2014)
52.	Electrically-coupled Retzius neurons (Vazquez et al. 2009)
53.	Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014)
54.	Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011)
55.	Encoding and retrieval in a model of the hippocampal CA1 microcircuit (Cutsuridis et al. 2009)
56.	Engaging distinct oscillatory neocortical circuits (Vierling-Claassen et al. 2010)
57.	Escape response latency in the Giant Fiber System of Drosophila melanogastor (Augustin et al 2019)
58.	Excitatory and inhibitory interactions in populations of model neurons (Wilson and Cowan 1972)
59.	Feedforward heteroassociative network with HH dynamics (Lytton 1998)
60.	Fronto-parietal visuospatial WM model with HH cells (Edin et al 2007)
61.	Functional properties of dendritic gap junctions in Cerebellar Golgi cells (Szoboszlay et al. 2016)
62.	Gamma genesis in the basolateral amygdala (Feng et al 2019)
63.	Gamma oscillations in hippocampal interneuron networks (Bartos et al 2002)
64.	Gamma oscillations in hippocampal interneuron networks (Wang, Buzsaki 1996)
65.	H-currents effect on the fluctuation of gamma/beta oscillations (Avella-Gonzalez et al., 2015)
66.	High frequency oscillations in a hippocampal computational model (Stacey et al. 2009)
67.	Hippocampal basket cell gap junction network dynamics (Saraga et al. 2006)
68.	Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016)
69.	Hippocampus temporo-septal engram shift model (Lytton 1999)
70.	Hopfield and Brody model (Hopfield, Brody 2000)
71.	Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)
72.	Human L5 Cortical Circuit (Guet-McCreight)
73.	Human layer 2/3 cortical microcircuits in health and depression (Yao et al, 2022)
74.	Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013)
75.	In silico hippocampal modeling for multi-target pharmacotherapy in schizophrenia (Sherif et al 2020)
76.	Inferior Olive, subthreshold oscillations (Torben-Nielsen, Segev, Yarom 2012)
77.	Interaural time difference detection by slowly integrating neurons (Vasilkov Tikidji-Hamburyan 2012)
78.	Irregular oscillations produced by cyclic recurrent inhibition (Friesen, Friesen 1994)
79.	Irregular spiking in NMDA-driven prefrontal cortex neurons (Durstewitz and Gabriel 2006)
80.	JitCon: Just in time connectivity for large spiking networks (Lytton et al. 2008)
81.	Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011)
82.	Knox implementation of Destexhe 1998 spike and wave oscillation model (Knox et al 2018)
83.	L5 PFC microcircuit used to study persistent activity (Papoutsi et al. 2014, 2013)
84.	Large scale model of the olfactory bulb (Yu et al., 2013)
85.	Lateral dendrodenditic inhibition in the Olfactory Bulb (David et al. 2008)
86.	Learning spatial transformations through STDP (Davison, Frégnac 2006)
87.	Locust olfactory network with GGN and full KC population in the mushroom body (Ray et al 2020)
88.	Long time windows from theta modulated inhib. in entorhinal–hippo. loop (Cutsuridis & Poirazi 2015)
89.	MEG of Somatosensory Neocortex (Jones et al. 2007)
90.	Microcircuits of L5 thick tufted pyramidal cells (Hay & Segev 2015)
91.	Mitral cell activity gating by respiration and inhibition in an olfactory bulb NN (Short et al 2016)
92.	Model of arrhythmias in a cardiac cells network (Casaleggio et al. 2014)
93.	Model of CA1 activity during working memory task (Spera et al. 2016)
94.	Model of the cerebellar granular network (Sudhakar et al 2017)
95.	Modeling local field potentials (Bedard et al. 2004)
96.	Modelling platform of the cochlear nucleus and other auditory circuits (Manis & Compagnola 2018)
97.	Modulation of hippocampal rhythms by electric fields and network topology (Berzhanskaya et al. 2013)
98.	Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014)
99.	Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017)
100.	Multiplication by NMDA receptors in Direction Selective Ganglion cells (Poleg-Polsky & Diamond 2016)
101.	Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016)
102.	Muscle spindle feedback circuit (Moraud et al, 2016)
103.	Neocort. pyramidal cells subthreshold somatic voltage controls spike propagation (Munro Kopell 2012)
104.	Network recruitment to coherent oscillations in a hippocampal model (Stacey et al. 2011)
105.	Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)
106.	Nonlinear dendritic processing in barrel cortex spiny stellate neurons (Lavzin et al. 2012)
107.	Normal ripples, abnormal ripples, and fast ripples in a hippocampal model (Fink et al. 2015)
108.	Olfactory bulb cluster formation (Migliore et al. 2010)
109.	Olfactory bulb mitral and granule cell column formation (Migliore et al. 2007)
110.	Olfactory bulb mitral and granule cell: dendrodendritic microcircuits (Migliore and Shepherd 2008)
111.	Olfactory bulb mitral cell gap junction NN model: burst firing and synchrony (O`Connor et al. 2012)
112.	Olfactory bulb mitral cell: synchronization by gap junctions (Migliore et al 2005)
113.	Olfactory Bulb Network (Davison et al 2003)
114.	Olfactory Computations in Mitral-Granule cell circuits (Migliore & McTavish 2013)
115.	Oscillating neurons in the cochlear nucleus (Bahmer Langner 2006a, b, and 2007)
116.	Parallel network simulations with NEURON (Migliore et al 2006)
117.	Parallel odor processing by mitral and middle tufted cells in the OB (Cavarretta et al 2016, 2018)
118.	Parallelizing large networks in NEURON (Lytton et al. 2016)
119.	Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012)
120.	Parvalbumin-positive basket cells differentiate among hippocampal pyramidal cells (Lee et al. 2014)
121.	Phase response theory in sparsely + strongly connected inhibitory NNs (Tikidji-Hamburyan et al 2019)
122.	PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
123.	Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)
124.	pre-Bötzinger complex variability (Fietkiewicz et al. 2016)
125.	Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)
126.	Purkinje cell: Synaptic activation predicts voltage control of burst-pause (Masoli & D'Angelo 2017)
127.	Purkinje neuron network (Zang et al. 2020)
128.	Pyramidal neuron, fast, regular, and irregular spiking interneurons (Konstantoudaki et al 2014)
129.	Regulation of a slow STG rhythm (Nadim et al 1998)
130.	Reinforcement learning of targeted movement (Chadderdon et al. 2012)
131.	Response properties of neocort. neurons to temporally modulated noisy inputs (Koendgen et al. 2008)
132.	Role for short term plasticity and OLM cells in containing spread of excitation (Hummos et al 2014)
133.	SCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)
134.	Sensorimotor cortex reinforcement learning of 2-joint virtual arm reaching (Neymotin et al. 2013)
135.	Sensory-evoked responses of L5 pyramidal tract neurons (Egger et al 2020)
136.	Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014)
137.	Single compartment Dorsal Lateral Medium Spiny Neuron w/ NMDA and AMPA (Biddell and Johnson 2013)
138.	Single E-I oscillating network with amplitude modulation (Avella Gonzalez et al. 2012)
139.	Small world networks of Type I and Type II Excitable Neurons (Bogaard et al. 2009)
140.	Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation (Luque et al 2019)
141.	Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011)
142.	Spinal Dorsal Horn Network Model (Medlock et al 2022)
143.	State dependent drug binding to sodium channels in the dentate gyrus (Thomas & Petrou 2013)
144.	Status epilepticus alters dentate basket cell tonic inhibition (Yu J et al 2013)
145.	Stoney vs Histed: Quantifying spatial effects of intracortical microstims (Kumaravelu et al 2022)
146.	Storing serial order in intrinsic excitability: a working memory model (Conde-Sousa & Aguiar 2013)
147.	Synaptic gating at axonal branches, and sharp-wave ripples with replay (Vladimirov et al. 2013)
148.	Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010)
149.	Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013)
150.	Synchrony by synapse location (McTavish et al. 2012)
151.	Thalamic network model of deep brain stimulation in essential tremor (Birdno et al. 2012)
152.	Thalamic quiescence of spike and wave seizures (Lytton et al 1997)
153.	Thalamic Reticular Network (Destexhe et al 1994)
154.	Thalamocortical and Thalamic Reticular Network (Destexhe et al 1996)
155.	Thalamocortical augmenting response (Bazhenov et al 1998)
156.	The virtual slice setup (Lytton et al. 2008)
157.	Tonic-clonic transitions in a seizure simulation (Lytton and Omurtag 2007)
158.	Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008)
159.	Updated Tritonia Swim CPG (Calin-Jagemann et al. 2007)

Re-display model names with descriptions