Models that contain the Modeling Application : Python (Home Page)

("Python is a dynamic object-oriented programming language that can be used for many kinds of software development. It offers strong support for integration with other languages and tools, comes with extensive standard libraries, and can be learned in a few days. Many Python programmers report substantial productivity gains and feel the language encourages the development of higher quality, more maintainable code. ...")
Re-display model names with descriptions
    Models
1.  3D olfactory bulb: operators (Migliore et al, 2015)
2.  3D-printer visualization of NEURON models (McDougal and Shepherd, 2015)
3.  A contracting model of the basal ganglia (Girard et al. 2008)
4.  A detailed Purkinje cell model (Masoli et al 2015)
5.  A general model of hippocampal and dorsal striatal learning and decision making (Geerts et al 2020)
6.  A model of ASIC1a and synaptic cleft pH modulating wind-up in wide dynamic range neurons (Delrocq)
7.  A model of optimal learning with redundant synaptic connections (Hiratani & Fukai 2018)
8.  A network of AOB mitral cells that produces infra-slow bursting (Zylbertal et al. 2017)
9.  A simple model of neuromodulatory state-dependent synaptic plasticity (Pedrosa and Clopath, 2016)
10.  A single-cell spiking model for the origin of grid-cell patterns (D'Albis & Kempter 2017)
11.  A spatial model of the intermediate superior colliculus (Moren et. al. 2013)
12.  A synapse model for developing somatosensory cortex (Manninen et al 2020)
13.  Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011)
14.  Acetylcholine Boosts Dendritic NMDA Spikes in a CA3 Pyramidal Neuron Model (Humphries et al., 2021)
15.  Action potential-evoked Na+ influx similar in axon and soma (Fleidervish et al. 2010) (Python)
16.  Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)
17.  Adaptive dual control of deep brain stimulation in Parkinsons disease simulations (Grado et al 2018)
18.  Allen Institute: Gad2-IRES-Cre VISp layer 5 472447460
19.  Allen Institute: Gad2-IRES-Cre VISp layer 5 473561729
20.  Allen Institute: Htr3a-Cre VISp layer 2/3 472352327
21.  Allen Institute: Htr3a-Cre VISp layer 2/3 472421285
22.  Allen Institute: Nr5a1-Cre VISp layer 2/3 473862496
23.  Allen Institute: Nr5a1-Cre VISp layer 4 329322394
24.  Allen Institute: Nr5a1-Cre VISp layer 4 472306544
25.  Allen Institute: Nr5a1-Cre VISp layer 4 472442377
26.  Allen Institute: Nr5a1-Cre VISp layer 4 472451419
27.  Allen Institute: Nr5a1-Cre VISp layer 4 472915634
28.  Allen Institute: Nr5a1-Cre VISp layer 4 473834758
29.  Allen Institute: Nr5a1-Cre VISp layer 4 473863035
30.  Allen Institute: Nr5a1-Cre VISp layer 4 473871429
31.  Allen Institute: Ntsr1-Cre VISp layer 4 472430904
32.  Allen Institute: Pvalb-IRES-Cre VISp layer 2/3 472306616
33.  Allen Institute: Pvalb-IRES-Cre VISp layer 5 471085845
34.  Allen Institute: Pvalb-IRES-Cre VISp layer 5 472349114
35.  Allen Institute: Pvalb-IRES-Cre VISp layer 5 472912177
36.  Allen Institute: Pvalb-IRES-Cre VISp layer 5 473465774
37.  Allen Institute: Pvalb-IRES-Cre VISp layer 5 473862421
38.  Allen Institute: Pvalb-IRES-Cre VISp layer 6a 471081668
39.  Allen Institute: Pvalb-IRES-Cre VISp layer 6a 472301074
40.  Allen Institute: Pvalb-IRES-Cre VISp layer 6a 473860269
41.  Allen Institute: Rbp4-Cre VISp layer 5 472424854
42.  Allen Institute: Rbp4-Cre VISp layer 6a 473871592
43.  Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472299294
44.  Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472434498
45.  Allen Institute: Rorb-IRES2-Cre-D VISp layer 4 473863510
46.  Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 471087975
47.  Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 473561660
48.  Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472300877
49.  Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472427533
50.  Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472912107
51.  Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 473465456
52.  Allen Institute: Scnn1a-Tg2-Cre VISp layer 5 472306460
53.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 329321704
54.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 472363762
55.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473862845
56.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473872986
57.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 472455509
58.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473863578
59.  Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473871773
60.  Allen Institute: Sst-IRES-Cre VISp layer 2/3 471086533
61.  Allen Institute: Sst-IRES-Cre VISp layer 2/3 472304676
62.  Allen Institute: Sst-IRES-Cre VISp layer 4 472304539
63.  Allen Institute: Sst-IRES-Cre VISp layer 5 472299363
64.  Allen Institute: Sst-IRES-Cre VISp layer 5 472450023
65.  Allen Institute: Sst-IRES-Cre VISp layer 5 473835796
66.  Allen Institute: Sst-IRES-Cre VISp layer 6a 472440759
67.  An attractor network model of grid cells and theta-nested gamma oscillations (Pastoll et al 2013)
68.  Analytical modelling of temperature effects on an AMPA-type synapse (Kufel & Wojcik 2018)
69.  AOB mitral cell: persistent activity without feedback (Zylbertal et al., 2015)
70.  Automated metadata suggester (McDougal et al 2018)
71.  Ave. neuron model for slow-wave sleep in cortex Tatsuki 2016 Yoshida 2018 Rasmussen 2017 (all et al)
72.  Biophysical model for field potentials of networks of I&F neurons (beim Graben & Serafim 2013)
73.  Biophysically detailed model of somatosensory thalamocortical circuit
74.  Boolean network-based analysis of the apoptosis network (Mai and Liu 2009)
75.  Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017)
76.  Brette-Gerstner model (Touboul and Brette 2008)
77.  CA1 PV+ fast-firing hippocampal interneuron (Ferguson et al. 2013)
78.  CA1 pyr cell: Inhibitory modulation of spatial selectivity+phase precession (Grienberger et al 2017)
79.  CA1 pyr cell: phenomenological NMDAR-based model of synaptic plasticity (Dainauskas et al 2023)
80.  CA1 pyramidal cell receptor dependent cAMP dynamics (Chay et al. 2016)
81.  CA1 pyramidal neuron (Ferguson et al. 2014)
82.  CA1 pyramidal neuron network model (Ferguson et al 2015)
83.  CA1 SOM+ (OLM) hippocampal interneuron (Ferguson et al. 2015)
84.  Ca2+ oscillations in single astrocytes (Lavrentovich and Hemkin 2008) (python) (Manninen et al 2017)
85.  CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)
86.  Calculating the consequences of left-shifted Nav channel activity in sick cells (Joos et al 2018)
87.  Cellular and Synaptic Mechanisms Differentiate Mitral & Superficial Tufted Cells (Jones et al 2020)
88.  Central Nervous System tadpole model in Matlab and NEURON-Python (Ferrario et al, 2021)
89.  Cerebellar granule cell (Masoli et al 2020)
90.  CN bushy, stellate neurons (Rothman, Manis 2003) (Brian 2)
91.  CN bushy, stellate neurons (Rothman, Manis 2003) (Brian)
92.  Code to calc. spike-trig. ave (STA) conduct. from Vm (Pospischil et al. 2007, Rudolph et al. 2007)
93.  Coincident signals in Olfactory Bulb Granule Cell spines (Aghvami et al 2019)
94.  Comparison of DA-based Stochastic Algorithms (Pezo et al. 2014)
95.  Composite spiking network/neural field model of Parkinsons (Kerr et al 2013)
96.  Computational modeling of gephyrin-dependent inhibitory transsynaptic signaling (Lupascu et al 2020)
97.  Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017)
98.  Computing with neural synchrony (Brette 2012)
99.  Concentration dependent nonlinear K+ and Cl- leak current (Huang et al. 2015)
100.  Conductance-based model of rodent thoracic sympathetic postganglionic neuron (McKinnon et al 2019)
101.  Connection-set Algebra (CSA) for the representation of connectivity in NN models (Djurfeldt 2012)
102.  Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013)
103.  Cortical Basal Ganglia Network Model during Closed-loop DBS (Fleming et al 2020)
104.  Cortical feedback alters visual response properties of dLGN relay cells (Martínez-Cañada et al 2018)
105.  CRH modulates excitatory transmission and network physiology in hippocampus (Gunn et al. 2017)
106.  Current Dipole in Laminar Neocortex (Lee et al. 2013)
107.  Dendritic Impedance in Neocortical L5 PT neurons (Kelley et al. 2021)
108.  Dentate Gyrus model including Granule cells with dendritic compartments (Chavlis et al 2017)
109.  Depolarization Enhacement of Dendritic Spike Propagation (Bock et al 2022)
110.  Diffusive homeostasis in a spiking network model (Sweeney et al. 2015)
111.  Distal inhibitory control of sensory-evoked excitation (Egger, Schmitt et al. 2015)
112.  Dorsal Column Fiber Stimulation model (Gilbert et al. 2022)
113.  Duration-tuned neurons from the inferior colliculus of vertebrates (Aubie et al. 2012)
114.  Earthworm medial giant fiber conduction velocity across electrical synapses (Heller, Crisp 2016)
115.  Effect of polysynaptic facilitaiton between piriform-hippocampal network stages (Trieu et al 2015)
116.  Efficient simulation of 3D reaction-diffusion in models of neurons (McDougal et al, 2022)
117.  Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014)
118.  ELL Medium Ganglion Cell (Mormyrid fish) (Muller et al, accepted)
119.  ELL Medium Ganglion cell (Muller et al 2019)
120.  Endocannabinoid dynamics gate spike-timing dependent depression and potentiation (Cui et al 2016)
121.  Excitatory synaptic interactions in pyramidal neuron dendrites (Behabadi et al. 2012)
122.  Explainable AI for spatial navigation based on hippocampal circuitry (Coppolino + Migliore 2023)
123.  Fast Spiking Basket cells (Tzilivaki et al 2019)
124.  Feedforward network undergoing Up-state-mediated plasticity (Gonzalez-Rueda et al. 2018)
125.  Firing patterns of CA3 hippocampal neurons (Soldado-Magraner et al. 2019)
126.  Fully continuous Pinsky-Rinzel model for bifurcation analysis (Atherton et al. 2016)
127.  Functional balanced networks with synaptic plasticity (Sadeh et al, 2015)
128.  Gamma-beta alternation in the olfactory bulb (David, Fourcaud-Trocmé et al., 2015)
129.  Gap junction plasticity as a mechanism to regulate network-wide oscillations (Pernelle et al 2018)
130.  Glutamate mediated dendritic and somatic plateau potentials in cortical L5 pyr cells (Gao et al '20)
131.  Glutamate-evoked Ca2+ oscillations in single astrocytes (De Pitta et al. 2009) (Manninen et al 2017)
132.  Glutamate-evoked Ca2+ oscillations in single astrocytes (Modified from Dupont et al. 2011)
133.  Goldfish Mauthner cell (Medan et al 2017)
134.  Grid cell-to-place cell transformation model w AD-related synaptic loss (Ness and Schultz 2021)
135.  Hierarchical network model of perceptual decision making (Wimmer et al 2015)
136.  Hippocampal CA1 pyramidal cell demonstrating dynamic mode switching (Berteau & Bullock 2020)
137.  Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)
138.  Human auditory periphery model: cochlea, IHC-AN, auditory brainstem responses (Verhulst et al 2018)
139.  Human L2/3 pyramidal cells with low Cm values (Eyal et al. 2016)
140.  Hyperexcitability from Nav1.2 channel loss in neocortical pyramidal cells (Spratt et al 2021)
141.  Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013)
142.  Impedance spectrum in cortical tissue: implications for LFP signal propagation (Miceli et al. 2017)
143.  In vivo imaging of dentate gyrus mossy cells in behaving mice (Danielson et al 2017)
144.  Information transmission in cerebellar granule cell models (Rossert et al. 2014)
145.  Inhibition of bAPs and Ca2+ spikes in a multi-compartment pyramidal neuron model (Wilmes et al 2016)
146.  Inhibitory neuron plasticity as a mechanism for ocular dominance plasticity (Bono & Clopath 2019)
147.  Inhibitory plasticity balances excitation and inhibition (Vogels et al. 2011)
148.  Input strength and time-varying oscillation peak frequency (Cohen MX 2014)
149.  Interplay between somatic and dendritic inhibition promotes place fields (Pedrosa & Clopath 2020)
150.  Kernel method to calculate LFPs from networks of point neurons (Telenczuk et al 2020)
151.  Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011)
152.  Large-scale neural model of visual short-term memory (Ulloa, Horwitz 2016; Horwitz, et al. 2005,...)
153.  Layer V pyramidal cell functions and schizophrenia genetics (Mäki-Marttunen et al 2019)
154.  Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018)
155.  LCN-HippoModel: model of CA1 PCs deep-superficial theta firing dynamics (Navas-Olive et al 2020)
156.  Leaky Integrate and Fire Neuron Model of Context Integration (Calvin, Redish 2021)
157.  LFP in striatum (Tanaka & Nakamura 2019)
158.  Library of biophysically detailed striatal projection neurons (Lindroos and Hellgren Kotaleski 2020)
159.  Locus Coeruleus blocking model (Chowdhury et al.)
160.  Maximal firing rate in midbrain dopamine neurons (Knowlton et al., 2021)
161.  Mean field model for Hodgkin Huxley networks of neurons (Carlu et al 2020)
162.  Mean-Field models of conductance-based NNs of spiking neurons with adaptation (di Volo et al 2019)
163.  MEC layer II stellate cell: Synaptic mechanisms of grid cells (Schmidt-Hieber & Hausser 2013)
164.  Mechanisms underlying subunit independence in pyramidal neuron dendrites (Behabadi and Mel 2014)
165.  Memory savings through unified pre- and postsynaptic STDP (Costa et al 2015)
166.  Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018)
167.  Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018) (PyNN)
168.  Minimal model of interictal and ictal discharges “Epileptor-2” (Chizhov et al 2018)
169.  Model of eupnea and sigh generation in respiratory network (Toporikova et al 2015)
170.  Model of peripheral nerve with ephaptic coupling (Capllonch-Juan & Sepulveda 2020)
171.  Model of peristalsis in the dorsal blood vessel of Lumbriculus variegatus (Halfmann and Crisp 2011)
172.  Model of Type 3 firing in neurons (Clay et al 2008)
173.  Modeling a Nociceptive Neuro-Immune Synapse Activated by ATP and 5-HT in Meninges (Suleimanova et al., 2020)
174.  Modeling and MEG evidence of early consonance processing in auditory cortex (Tabas et al 2019)
175.  Modeling dendritic spikes and plasticity (Bono and Clopath 2017)
176.  Modelling platform of the cochlear nucleus and other auditory circuits (Manis & Compagnola 2018)
177.  Modelling the effects of short and random proto-neural elongations (de Wiljes et al 2017)
178.  Models of visual topographic map alignment in the Superior Colliculus (Tikidji-Hamburyan et al 2016)
179.  ModelView: online structural analysis of computational models (McDougal et al. 2015)
180.  Modular grid cell responses as a basis for hippocampal remapping (Monaco and Abbott 2011)
181.  Motion Clouds: Synthesis of random textures for motion perception (Leon et al. 2012)
182.  Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017)
183.  Multi-timescale adaptive threshold model (Kobayashi et al 2009) (NEURON)
184.  Multifunctional control of feeding in Aplysia (Webster-Wood et al. 2020)
185.  MultiScale Optimized Neuronal Intramembrane Cavitation (SONIC) model (Lemaire et al. 2019)
186.  Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013)
187.  Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016)
188.  Muscle spindle feedback circuit (Moraud et al, 2016)
189.  Na+ Signals in olfactory bulb neurons (granule cell model) (Ona-Jodar et al. 2017)
190.  Network bursts in cultured NN result from different adaptive mechanisms (Masquelier & Deco 2013)
191.  Network dynamics of electrically coupled pituitary cells (Fazli and Bertram, 2022)
192.  Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)
193.  Neural Field Simulator (Nichols & Hutt 2012-2015)
194.  Neural mass model based on single cell dynamics to model pathophysiology (Zandt et al 2014)
195.  NeuroGPU example on L5_TTPC1_cADpyr232_1 (Ben-Shalom 2022)(Ramaswamy et al., 2015)
196.  Neuromuscular network model of gut motility (Barth et al 2017)
197.  NEURON + Python (Hines et al. 2009)
198.  Olfactory bulb microcircuits model with dual-layer inhibition (Gilra & Bhalla 2015)
199.  Online learning model of olfactory bulb external plexiform layer network (Imam & Cleland 2020)
200.  Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012)
201.  Orientation selectivity in inhibition-dominated recurrent networks (Sadeh and Rotter, 2015)
202.  Oscillations, phase-of-firing coding and STDP: an efficient learning scheme (Masquelier et al. 2009)
203.  Parallel Tempering MCMC on Liu et al 1998 (Wang et al 2022)
204.  Perfect Integrate and fire with noisy adaptation or fractional noise (Richard et al 2018)
205.  Phase response curves firing rate dependency of rat purkinje neurons in vitro (Couto et al 2015)
206.  Phase response theory in sparsely + strongly connected inhibitory NNs (Tikidji-Hamburyan et al 2019)
207.  Phenomenological models of NaV1.5: Hodgkin-Huxley and kinetic formalisms (Andreozzi et al 2019)
208.  PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
209.  Place and grid cells in a loop (Rennó-Costa & Tort 2017)
210.  Pleiotropic effects of SCZ-associated genes (Mäki-Marttunen et al. 2017)
211.  PLS-framework (Tikidji-Hamburyan and Colonnese 2021)
212.  Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)
213.  PyMUS: A Python based Motor Unit Simulator (Kim & Kim 2018)
214.  Python demo of the VmT method to extract conductances from single Vm traces (Pospischil et al. 2009)
215.  Recurrent amplification of grid-cell activity (D'Albis and Kempter 2020)
216.  Reduced-morphology model of CA1 pyramidal cells optimized + validated w/ HippoUnit (Tomko et al '21)
217.  Resource competition in growing neurites (Hjorth et al 2014)
218.  Reward modulated STDP (Legenstein et al. 2008)
219.  Scaffold model of mouse CA1 hippocampus. (Gandolfi et al 2022)
220.  Schiz.-linked gene effects on intrinsic single-neuron excitability (Maki-Marttunen et al. 2016)
221.  SCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)
222.  SCZ-associated variant effects on L5 pyr cell NN activity and delta osc. (Maki-Marttunen et al 2018)
223.  Self-organization of cortical areas in development and evolution of neocortex (Imam & Finlay 2021)
224.  Sensory feedback in an oscillatory interference model of place cell activity (Monaco et al. 2011)
225.  Sensory-evoked responses of L5 pyramidal tract neurons (Egger et al 2020)
226.  Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014)
227.  Simulation of calcium signaling in fine astrocytic processes (Denizot et al 2019)
228.  Single Trial Sequence learning: a spiking neurons model based on hippocampus (Coppolino et al 2021)
229.  Somatodendritic consistency check for temporal feature segmentation (Asabuki & Fukai 2020)
230.  Sound-evoked activity in peripheral axons of type I spiral ganglion neurons (Budak et al. 2021)
231.  Sparse connectivity is required for decorrelation, pattern separation (Cayco-Gajic et al 2017)
232.  Spatial structure from diffusive synaptic plasticity (Sweeney and Clopath, 2016)
233.  Spike-Timing-Based Computation in Sound Localization (Goodman and Brette 2010)
234.  Spikelet generation and AP initiation in a L5 neocortical pyr neuron (Michalikova et al. 2017) Fig 1
235.  Spikelet generation and AP initiation in a simplified pyr neuron (Michalikova et al. 2017) Fig 3
236.  Spiny Projection Neuron Ca2+ based plasticity is robust to in vivo spike train (Dorman&Blackwell)
237.  Spontaneous calcium oscillations in single astrocytes (Riera et al. 2011) (Manninen et al 2017)
238.  Spontaneous weakly correlated excitation and inhibition (Tan et al. 2013)
239.  STDP allows fast rate-modulated coding with Poisson-like spike trains (Gilson et al. 2011)
240.  STDP and oscillations produce phase-locking (Muller et al. 2011)
241.  Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) (pylab)
242.  Striatal D1R medium spiny neuron, including a subcellular DA cascade (Lindroos et al 2018)
243.  Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013)
244.  Switching circuit for optimal context integration during static + moving contexts (Voina et al 2022)
245.  Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013)
246.  Synchronized oscillations of clock gene expression in the choroid plexus (Myung et al 2018)
247.  Tag Trigger Consolidation (Clopath and Ziegler et al. 2008)
248.  The electrodiffusive Pinsky-Rinzel (edPR) model (Sætra et al., 2020)
249.  Theory and simulation of integrate-and-fire neurons driven by shot noise (Droste & Lindner 2017)
250.  TRPM8-dependent dynamic response in cold thermoreceptors (Olivares et al. 2015)
251.  Unsupervised learning of an efficient short-term memory network (Vertechi, Brendel & Machens 2014)
252.  Ventromedial Thalamocortical Neuron (Bichler et al 2021)
253.  Vertical System (VS) tangential cells network model (Trousdale et al. 2014)
254.  Voltage-based STDP synapse (Clopath et al. 2010)
255.  Voltage-gated conductances can counteract filtering effect of membrane capacitance (Heras et al '16)

Re-display model names with descriptions