Simulation Environment: MATLAB

Note: this list includes both models hosted here at ModelDB and models where have metadata and link to the sourcecode somewhere else. These may also be viewed separately; see the browse by simulator page.

  1. A basal ganglia model of aberrant learning (Ursino et al. 2018)
  2. A biophysical model of vestibular ganglion neurons (Hight & Kalluri 2016, Ventura & Kalluri 2018)
  3. A bistable model of Spike-Wave seizure and background activity (Taylor et al. 2014)
  4. A Computational Model for the Binocular Vector Disparity Estimation (Chessa & Solari 2018)
  5. A computational model of a small DRG neuron to explore pain (Verma et al. 2019, 2020)
  6. A computational model of action selection in the basal ganglia (Suryanarayana et al 2019)
  7. A computational model of single-neuron perturbations (Sadeh and Clopath 2020)
  8. A cortical sheet mesoscopic model for investigating focal seizure onset dynamics (Wang et al. 2014)
  9. A detailed data-driven network model of prefrontal cortex (Hass et al 2016)
  10. A generic MAPK cascade model for random parameter sampling analysis (Mai and Liu 2013)
  11. A kinetic model unifying presynaptic short-term facilitation and depression (Lee et al. 2009)
  12. A mathematical model of a neurovascular unit (Dormanns et al 2015, 2016) (Farrs & David 2011)
  13. A mathematical model of evoked calcium dynamics in astrocytes (Handy et al 2017)
  14. A microcircuit model of the frontal eye fields (Heinzle et al. 2007)
  15. A model of local field potentials generated by medial superior olive neurons (Goldwyn et al 2014)
  16. A model of neurovascular coupling and the BOLD response (Mathias et al 2017, Kenny et al 2018)
  17. A model of rodent mechanoreceptors (LTMRs) (Medlock et al., 2024)
  18. A model of working memory for encoding multiple items (Ursino et al, in press)
  19. A modified Morris-Lecar model with gM and gAHP (Yang et al., 2022)
  20. A modified Morris-Lecar with TRPC4 & GIRK (Tian et al. 2022)
  21. A multiphysics neuron model for cellular volume dynamics (Lee et al. 2011)
  22. A Neural mass computational model of the Thalamocorticothalamic circuitry (Bhattacharya et al. 2011)
  23. A neural mass model for critical assessment of brain connectivity (Ursino et al 2020)
  24. A neural model of Parkinson`s disease (Cutsuridis and Perantonis 2006, Cutsuridis 2006, 2007)
  25. A neural network model of mathematics anxiety: The role of attention (Rose et al., 2023)
  26. A neuronal circuit simulator for non Monte Carlo analysis of neuronal noise (Kilinc & Demir 2018)
  27. A novel mechanism for ramping bursts based on slow negative feedback in model respiratory neurons (John et al., accepted)
  28. A simulation method for the firing sequences of motor units (Jiang et al 2006)
  29. A spatially extended model for macroscopic spike-wave discharges (Taylor and Baier 2011)
  30. A spiking model of cortical broadcast and competition (Shanahan 2008)
  31. A state-space model to quantify common input to motor neurons (Feeney et al 2017)
  32. A two-layer biophysical olfactory bulb model of cholinergic neuromodulation (Li and Cleland 2013)
  33. Acetylcholine-modulated plasticity in reward-driven navigation (Zannone et al 2018)
  34. ACh modulation in olfactory bulb and piriform cortex (de Almeida et al. 2013;Devore S, et al. 2014)
  35. Activator protein 1(AP-1) transcriptional regulatory model in brainstem neurons (Makadia et al 2015)
  36. Active intrinsic conductances in networks, transients, activity, plasticity (Akosy and Shouval 2021)
  37. Activity dependent changes in dendritic spine density and spine structure (Crook et al. 2007)
  38. Adaptation of Short-Term Plasticity parameters (Esposito et al. 2015)
  39. Ambiguous Encoding and Distorted Perception (Carlson and Kawasaki 2006)
  40. An integrated deep learning-based model of spatial cells that combines self-motion with sensory information (Aziz et al., 2022)
  41. An ODE model of the inspiratory & sigh rhythms (Borrus et al., 2024)
  42. An oscillatory neural autoencoder based on frequency modulation and multiplexing (Soman et al 2018)
  43. Artificial neuron model (Izhikevich 2003, 2004, 2007)
  44. Astrocyte and Blood Vessel Calcium Imaging Tracking code (Haidey et al 2021)
  45. Auditory nerve model for predicting performance limits (Heinz et al 2001)
  46. Auditory nerve model with linear tuning (Heinz et al 2001)
  47. Auditory nerve response model (Tan, Carney 2003)
  48. Axon growth model (Diehl et al. 2016)
  49. Axonal HH-model for temperature stimulation (Fribance et al 2016)
  50. Balance of excitation and inhibition (Carvalho and Buonomano 2009)
  51. Basal Ganglia and Levodopa Pharmacodynamics model for parameter estimation in PD (Ursino et al 2020)
  52. Basal ganglia motor function and the inverse kinematics calculation (Salimi-Badr et al 2017)
  53. Basal ganglia-corticothalamic (BGCT) network (Chen et al., 2014)
  54. Basal ganglia-thalamic network model for deep brain stimulation (So et al. 2012)
  55. Basal ganglia-thalamocortical loop model of action selection (Humphries and Gurney 2002)
  56. Binocular energy model set for binocular neurons in optic lobe of praying mantis (Rosner et al 2019)
  57. BK - CaV coupling (Montefusco et al. 2017)
  58. Breakdown of accmmodation in nerve: a possible role for INAp (Hennings et al 2005)
  59. Bump Attractor Models: Delayed Response & Recognition Span - spatial condition (Ibanez et al 2019)
  60. Burst and tonic firing behaviour in subfornical organ (SFO) neurons (Medlock et al 2018)
  61. Bursting and oscillations in RD1 Retina driven by AII Amacrine Neuron (Choi et al. 2014)
  62. CA1 pyramidal cells, basket cells, ripples (Malerba et al 2016)
  63. CA1 pyramidal neuron dendritic spine with plasticity (O`Donnell et al. 2011)
  64. CA1 pyramidal: Stochastic amplification of KCa in Ca2+ microdomains (Stanley et al. 2011)
  65. CA3 Radiatum/Lacunosum-Moleculare interneuron, Ih (Anderson et al. 2011)
  66. Calyx of Held, short term plasticity (Yang Z et al. 2009)
  67. Cancelling redundant input in ELL pyramidal cells (Bol et al. 2011)
  68. Cardiac models of circadian rhythms in early afterdepolarizations & arrhythmias (Diekman & Wei 2021)
  69. Cell signaling/ion channel variability effects on neuronal response (Anderson, Makadia, et al. 2015)
  70. Central Nervous System tadpole model in Matlab and NEURON-Python (Ferrario et al, 2021)
  71. Cholinergic and nicotinic regulation of DA neuron firing (Morozova et al 2020)
  72. Circadian clock model based on protein sequestration (simple version) (Kim & Forger 2012)
  73. Circadian clock model in mammals (detailed version) (Kim & Forger 2012)
  74. Coding explains development of binocular vision and its failure in Amblyopia (Eckmann et al 2020)
  75. Coincidence detection in MSO principal cells (Goldwyn et al. 2019)
  76. Cold-Temperature Coding with Bursting and Spiking Based on TRP Channel Dynamics in Drosophila Larva Sensory Neurons (Maksymchuk, N., A. Sakurai, D.N. Cox, and G.S. Cymbalyuk, 2023)
  77. Combination sensitivity and active conductances (Carlson and Kawasaki 2006)
  78. Comparing correlation responses to motion estimation models (Salazar-Gatzimas et al. 2016)
  79. Competing oscillator 5-cell circuit and Parameterscape plotting (Gutierrez et al. 2013)
  80. Composite spiking network/neural field model of Parkinsons (Kerr et al 2013)
  81. Computational endophenotypes in addiction (Fiore et al 2018)
  82. Computational modeling of ultrasonic Subthalamic Nucleus stimulation (Tarnaud et al 2019)
  83. Computational modelling of channelrhodopsin-2 photocurrent characteristics (Stefanescu et al. 2013)
  84. Conditions for synaptic specificity in maintenance phase of synaptic plasticity (Huertas et al, '22)
  85. CONFIGR: a vision-based model for long-range figure completion (Carpenter et al. 2007)
  86. Continuous time stochastic model for neurite branching (van Elburg 2011)
  87. Continuum model of tubulin-driven neurite elongation (Graham et al 2006)
  88. Convergence regulates synchronization-dependent AP transfer in feedforward NNs (Sailamul et al 2017)
  89. Core respiratory network organization: Insights from optogenetics and modeling (Ausborn et al 2018)
  90. Cortex-Basal Ganglia-Thalamus network model (Kumaravelu et al. 2016)
  91. Cortico - Basal Ganglia Loop (Mulcahy et al 2020)
  92. Cortico-striatal plasticity in medium spiny neurons (Gurney et al 2015)
  93. Decoding movement trajectory from simulated grid cell population activity (Bush & Burgess 2019)
  94. Deep belief network learns context dependent behavior (Raudies, Zilli, Hasselmo 2014)
  95. Dendritic Na inactivation drives a decrease in ISI (Fernandez et al 2005)
  96. Dendritic properties control energy efficiency of APs in cortical pyramidal cells (Yi et al 2017)
  97. Detailed analysis of trajectories in the Morris water maze (Gehring et al. 2015)
  98. Development and Binocular Matching of Orientation Selectivity in Visual Cortex (Xu et al 2020)
  99. Dipole Localization Kit (Mechler & Victor, 2012)
  100. Direct recruitment of S1 pyramidal cells and interneurons via ICMS (Overstreet et al., 2013)
  101. Disentangling astroglial physiology with a realistic cell model in silico (Savtchenko et al 2018)
  102. Distributed cerebellar plasticity implements adaptable gain control (Garrido et al., 2013)
  103. Distributed representation of perceptual categories in the auditory cortex (Kim and Bao 2008)
  104. Distributed synaptic plasticity and spike timing (Garrido et al. 2013)
  105. Distributed working memory in large-scale macaque brain model (Mejias and Wang, 2022)
  106. Dopamine-modulated medium spiny neuron, reduced model (Humphries et al. 2009)
  107. Drosophila 3rd instar larval aCC motoneuron (Gunay et al. 2015)
  108. Drosophila circadian clock neurone model of essential tremor (Smith et al 2018)
  109. Drosophila lateral ventral clock neuron (LNV) model (Smith et al 2019)
  110. E-I balance modulates formation and dynamics of neuronal assemblies (Sadeh and Clopath, 2021)
  111. Effect of circuit structure on odor representation in insect olfaction (Rajagopalan & Assisi 2020)
  112. Effect of cortical D1 receptor sensitivity on working memory maintenance (Reneaux & Gupta 2018)
  113. Effect of ionic diffusion on extracellular potentials (Halnes et al 2016)
  114. Effects of the membrane AHP on the Lateral Superior Olive (LSO) (Zhou & Colburn 2010)
  115. Efficient estimation of detailed single-neuron models (Huys et al. 2006)
  116. Electrical activity of the suprachiasmatic nuclei (Stinchcombe et al. 2017)
  117. Electrodiffusive astrocytic and extracellular ion concentration dynamics model (Halnes et al. 2013)
  118. Elementary mechanisms producing facilitation of Cav2.1 (P/Q-type) channels
  119. ELL Medium Ganglion Cell (Mormyrid fish) (Muller et al, 2023)
  120. ELL pyramidal neuron (Simmonds and Chacron 2014)
  121. Emergence of Connectivity Motifs in Networks of Model Neurons (Vasilaki, Giugliano 2014)
  122. Entrainment and divisive inhibition in a neocortical neural mass model (Papasavvas et al 2020)
  123. Ephaptic coupling in passive cable and MSO neuron models (Goldwyn & Rinzel 2016)
  124. Epileptic seizure model with Morris-Lecar neurons (Beverlin and Netoff 2011)
  125. Equivalent excitability achieved via different Nav subtypes (Xie et al., 2024)
  126. Estimation of conductance in a conductance-based model of quadratic type (Vich & Guillamon 2015)
  127. Exact mean-field models for Izhikevich networks (Chen and Campbell 2022)
  128. Excessive beta oscillations in Parkinson's disease (Pavlides et al. 2015)
  129. Excitability of DA neurons and their regulation by synaptic input (Morozova et al. 2016a, 2016b)
  130. Excitation Properties of Computational Models of Unmyelinated Peripheral Axons (Pelot et al., 2021)
  131. Excitation-contraction coupling in an integrative heart cell model (Greenstein et al 2006)
  132. Excitotoxic loss of dopaminergic cells in PD (Muddapu et al 2019)
  133. Exploring the role of Kӧlliker-Fuse nucleus in breathing variability via mathematical modeling (John et al., 2023)
  134. External Tufted Cell Model (Ryan Viertel, Alla Borisyuk 2019)
  135. Extracellular Action Potential Simulations (Gold et al 2007)
  136. Extraction and classification of three cortical neuron types (Mensi et al. 2012)
  137. Failure of Deep Brain Stimulation in a basal ganglia neuronal network model (Dovzhenok et al. 2013)
  138. Fast population coding (Huys et al. 2007)
  139. Fast Spiking Basket cells (Tzilivaki et al 2019)
  140. Feature integration drives probabilistic behavior in Fly escape response (von Reyn et al 2017)
  141. FFV1MT: A V1-MT feedforward architecture for optical flow estimation (Solari et a., 2015)
  142. Fisher and Shannon information in finite neural populations (Yarrow et al. 2012)
  143. Fitting predictive coding to the neurophysiological data (Spratling 2019)
  144. Fractional leaky integrate-and-fire model (Teka et al. 2014)
  145. FRAT: An amygdala-centered model of fear conditioning (Krasne et al. 2011)
  146. Function and energy constrain neuronal biophysics in coincidence detection (Remme et al 2018)
  147. Gap junction coupled network of striatal fast spiking interneurons (Hjorth et al. 2009)
  148. Generation of granule cell dendritic morphology (Schneider et al. 2014)
  149. Generation of stable heading representations in diverse visual scenes (Kim et al 2019)
  150. Generic Bi-directional Real-time Neural Interface (Zrenner et al. 2010)
  151. Graph-theoretical Derivation of Brain Structural Connectivity (Giacopelli et al 2020)
  152. Grid cell model with compression effects (Raudies & Hasselmo, 2015)
  153. Grid cell oscillatory interference with noisy network oscillators (Zilli and Hasselmo 2010)
  154. Grid cell spatial firing models (Zilli 2012)
  155. Grid cells from place cells (Castro & Aguiar, 2014)
  156. Hebbian learning in a random network for PFC modeling (Lindsay, et al. 2017)
  157. Hebbian STDP for modelling the emergence of disparity selectivity (Chauhan et al 2018)
  158. HH model neuron of the Suprachiasmatic Nucleus including a persistent Na+ channel (Paul et al 2016)
  159. HH model of SCN neurons including a transient K+ channel (Bano-Otalora et al 2021)
  160. HH-type model of fast-spiking parvalbumin interneurons in spinal dorsal horn (Ma et al, 2023)
  161. Hierarchical anti-Hebbian network model for the formation of spatial cells in 3D (Soman et al 2019)
  162. Hierarchical Gaussian Filter (HGF) model of conditioned hallucinations task (Powers et al 2017)
  163. Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)
  164. Hippocampal spiking model for context dependent behavior (Raudies & Hasselmo 2014)
  165. Hodgkin–Huxley model with fractional gating (Teka et al. 2016)
  166. Homeostatic synaptic plasticity (Rabinowitch and Segev 2006a,b)
  167. Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)
  168. Human auditory periphery model: cochlea, IHC-AN, auditory brainstem responses (Verhulst et al 2018)
  169. Human sleep-wake regulatory network model (Gleit et al 2013, Booth et al 2017)
  170. Human tactile FA1 neurons (Hay and Pruszynski 2020)
  171. Hybrid NEURON-COMSOL sciatic nerve model with extracellular TIME stimulation (Xie et al, accepted)
  172. Hybrid oscillatory interference / continuous attractor NN of grid cell firing (Bush & Burgess 2014)
  173. Hyperbolic model (Daneshzand et al 2017)
  174. Hyperconnectivity, slow synapses in PFC mental retardation and autism model (Testa-Silva et al 2011)
  175. Hypothalamic CRH neurons represent physiological memory of positive and negative experience (Füzesi et al., 2023)
  176. I&F recurrent networks with current- or conductance-based synapses (Cavallari et al. 2014)
  177. IA and IT interact to set first spike latency (Molineux et al 2005)
  178. Impact of dendritic size and topology on pyramidal cell burst firing (van Elburg and van Ooyen 2010)
  179. Impact of Small Time Delays on the Onset of Oscillations and Synchrony (Al-Darabsah et al 2021)
  180. INa and IKv4.3 heterogeneity in canine LV myocytes (Flaim et al 2006)
  181. Inferring connection proximity in electrically coupled networks (Cali et al. 2007)
  182. Inhibition perturbations reveals dynamical structure of neural processing (Sadeh & Clopath 2020)
  183. Inhibitory control of motoneuron excitability (Venugopal et al 2011)
  184. Inhibitory plasticity balances excitation and inhibition (Vogels et al. 2011)
  185. Inner hair cell auditory nerve synapse model (Deligeorges, Mountain 1997)
  186. Input strength and time-varying oscillation peak frequency (Cohen MX 2014)
  187. Inverse stochastic resonance of cerebellar Purkinje cell (Buchin et al. 2016)
  188. Investigation of different targets in deep brain stimulation for Parkinson`s (Pirini et al. 2009)
  189. Irregular spiking in NMDA-driven prefrontal cortex neurons (Durstewitz and Gabriel 2006)
  190. L5 cortical neurons with recreated synaptic inputs in vitro correlation transfer (Linaro et al 2019)
  191. L5 pyr. cell spiking control by oscillatory inhibition in distal apical dendrites (Li et al 2013)
  192. Laminar analysis of excitatory circuits in vibrissal motor and sensory cortex (Hooks et al. 2011)
  193. Laminar connectivity matrix simulation (Weiler et al 2008)
  194. Large-scale laminar model of macaque cortex (Mejias et al 2016)
  195. Lateral dendrodenditic inhibition in the Olfactory Bulb (David et al. 2008)
  196. Layer 5 Pyramidal Neuron (Shai et al., 2015)
  197. Layer-specific pyramidal cell props underlie diverse ACC motor + limbic networks (Medalla et al '21)
  198. Leaky integrate-and-fire model of spike frequency adaptation in the LGMD (Gabbiani and Krapp 2006)
  199. Learning intrinsic excitability in Medium Spiny Neurons (Scheler 2014)
  200. Learning spatiotemporal sequences using recurrent spiking NN that discretizes time (Maes et al 2020)
  201. Leech Heart Interneuron model (Sharma et al 2020)
  202. Levodopa-Induced Toxicity in Parkinson's Disease (Muddapu et al, 2022)
  203. LGMD Variability and logarithmic compression in dendrites (Jones and Gabbiani, 2012, 2012B)
  204. LGNcircuit: Minimal LGN network model of temporal processing of visual input (Norheim et al. 2012)
  205. Lillie Transition: onset of saltatory conduction in myelinating axons (Young et al. 2013)
  206. Linking STDP and Dopamine action to solve the distal reward problem (Izhikevich 2007)
  207. Logarithmic distributions prove that intrinsic learning is Hebbian (Scheler 2017)
  208. Long- and short-term history effects in a spiking network model of statistical learning (Maes et al accepted)
  209. M1 and M4 intrinsically photosensitive retinal ganglion cells (Stinchcombe et al. 2021)
  210. Macroscopic model of epilepsy (Fietkiewicz & Loparo 2016)
  211. Markov Chain-based Stochastic Shielding Hodgkin Huxley Model (Schmandt, Galan 2012)
  212. Mathematical model for windup (Aguiar et al. 2010)
  213. Mathematical model of behavioral time scale plasticity (BTSP) of place fields (Shouval & Cone 2021)
  214. Maximum entropy model to predict spatiotemporal spike patterns (Marre et al. 2009)
  215. Mean Field Equations for Two-Dimensional Integrate and Fire Models (Nicola and Campbell, 2013)
  216. Mean-field systems and small scale neural networks (Ferguson et al. 2015)
  217. Mechanisms of magnetic stimulation of central nervous system neurons (Pashut et al. 2011)
  218. Mechanisms underlying different onset patterns of focal seizures (Wang Y et al 2017)
  219. Medial reticular formation of the brainstem: anatomy and dynamics (Humphries et al. 2006, 2007)
  220. Memory savings through unified pre- and postsynaptic STDP (Costa et al 2015)
  221. Method for deriving general HH neuron model`s spiking input-output relation (Soudry & Meir 2014)
  222. Microglial cytokine network (Anderson et al., 2015)
  223. Microsaccades and synchrony coding in the retina (Masquelier et al. 2016)
  224. Midbrain torus semicircularis neuron model (Aumentado-Armstrong et al. 2015)
  225. Model for concentration invariant odor coding based on primacy hypothesis (Wilson et al 2017)
  226. Model of AngII signaling and membrane electrophysiology (Makadia, Anderson, Fey et al., 2015)
  227. Model of calcium oscillations in olfactory cilia (Reidl et al. 2006)
  228. Model of cerebellar parallel fiber-Purkinje cell LTD and LTP (Gallimore et al 2018)
  229. Model of cochlear membrane adapted (Peterson, Bogert 1950)
  230. Model of long range transmission of gamma oscillation (Murray 2007)
  231. Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014)
  232. Model of working memory based on negative derivative feedback (Lim and Goldman, 2013)
  233. Model predictive control model for an isometric motor task (Ueyama 2017)
  234. Modeling and MEG evidence of early consonance processing in auditory cortex (Tabas et al 2019)
  235. Modeling extracellular electrical stimulation (Tahayori et al. 2012)
  236. Modeling hebbian and homeostatic plasticity (Toyoizumi et al. 2014)
  237. Modelling enteric neuron populations and muscle fed-state motor patterns (Chambers et al. 2011)
  238. Modelling gain modulation in stability-optimised circuits (Stroud et al 2018)
  239. Models for cortical UP-DOWN states in a bistable inhibitory-stabilized network (Jercog et al 2017)
  240. Models of Vector Navigation with Grid Cells (Bush et al., 2015)
  241. Motoneuron model of self-sustained firing after spinal cord injury (Kurian et al. 2011)
  242. Motoneuron simulations for counting motor units (Major and Jones 2005)
  243. Motor Cortex Connectivity & Event Related Desynchronization Based on Neural Mass Models (Ursino 21)
  244. Mouse colorectal afferent ending (Feng et al 2015)
  245. Multifunctional control of feeding in Aplysia (Webster-Wood et al. 2020)
  246. Multiple mechanisms of short term plasticity at the calyx of Held (Hennig et al. 2008)
  247. Multiple modes of inner hair cell stimulation (Mountain, Cody 1999)
  248. Multiscale model of excitotoxicity in PD (Muddapu and Chakravarthy 2020)
  249. Multisensory integration in the superior colliculus: a neural network model (Ursino et al. 2009)
  250. Myelin dystrophy impairs signal transmission and working memory in a multiscale model of the aging prefrontal cortex (Ibañez, Sengupta et al., 2024)
  251. Neocort. pyramidal cells subthreshold somatic voltage controls spike propagation (Munro Kopell 2012)
  252. Network model of movement disorders (Yousif et al 2020)
  253. Network models of frequency modulated sweep detection (Skorheim et al. 2014)
  254. Neural mass model based on single cell dynamics to model pathophysiology (Zandt et al 2014)
  255. Neural Mass Model for relationship between Brain Rhythms + Functional Connectivity (Ricci et al '21)
  256. Neural mass model of the sleeping cortex (Weigenand et al 2014)
  257. Neural model of frog ventilatory rhythmogenesis (Horcholle-Bossavit and Quenet 2009)
  258. Neural transformations on spike timing information (Tripp and Eliasmith 2007)
  259. Neural-field model of generalized seizures (Zhao et al., 2015)
  260. Neurogenesis in the olfactory bulb controlled by top-down input (Adams et al 2018)
  261. Non-Weak E-Fields Pyramidal Neurons (Reznik et. al.,2015)
  262. Norns - Neural Network Studio (Visser & Van Gils 2014)
  263. Numerical Integration of Izhikevich and HH model neurons (Stewart and Bair 2009)
  264. Odor supported place cell model and goal navigation in rodents (Kulvicius et al. 2008)
  265. Olfactory bulb juxtaglomerular models (Carey et al., 2015)
  266. Olfactory Bulb mitral-granule network generates beta oscillations (Osinski & Kay 2016)
  267. Olfactory bulb network: neurogenetic restructuring and odor decorrelation (Chow et al. 2012)
  268. Olfactory receptor neuron model (Dougherty et al 2005)
  269. Opponent-channel model of the cortical representation of auditory space (Briley et al., 2012)
  270. Optimal Localist and Distributed Coding Through STDP (Masquelier & Kheradpisheh 2018)
  271. Optimal spatiotemporal spike pattern detection by STDP (Masquelier 2017)
  272. Origin of heterogeneous spiking patterns in spinal dorsal horn neurons (Balachandar & Prescott 2018)
  273. Oscillating neurons in the cochlear nucleus (Bahmer Langner 2006a, b, and 2007)
  274. Oscillation and coding in a proposed NN model of insect olfaction (Horcholle-Bossavit et al. 2007)
  275. Oscillations emerging from noise-driven NNs (Tchumatchenko & Clopath 2014)
  276. Oversampling method to extract excitatory and inhibitory conductances (Bedard et al. 2012)
  277. Pancreatic Beta Cell signalling pathways (Fridlyand & Philipson 2016) (MATLAB)
  278. Parallel cortical inhibition processing enables context-dependent behavior (Kuchibhotla et al. 2016)
  279. Parameter estimation for Hodgkin-Huxley based models of cortical neurons (Lepora et al. 2011)
  280. Particle-Swarm Based Modelling Reveals Two Distinct Classes of CRH^{PVN} Neurons (Lameu et al 2022)
  281. Patterns of synchronization in 2D networks of inhibitory neurons (Miller et al, 2022)
  282. Peripheral nerve:Morris-Lecar implementation of (Schwarz et al 1995)
  283. Phase oscillator models for lamprey central pattern generators (Varkonyi et al. 2008)
  284. Phase plane reveals two slow variables in midbrain dopamine neuron bursts (Yu and Canavier, 2015)
  285. Phase precession through acceleration of local theta rhythm (Castro & Aguiar 2011)
  286. Phase response curves firing rate dependency of rat purkinje neurons in vitro (Couto et al 2015)
  287. Phasic ACh promotes gamma oscillations in E-I networks (Lu et al, 2020)
  288. Phasic dopamine changes, Hebbian mechs during reversal learning in striatum (Schirru et al in press)
  289. Phenomenological model of the mouse circadian pacemaker (Cao et al., 2022)
  290. Pipette and membrane patch geometry effects on GABAa currents patch-clamp exps (Moroni et al. 2011)
  291. Plasticity forms non-overlapping adjacent ON and OFF RFs in cortical neurons (Sollini et al 2018)
  292. Pleiotropic effects of SCZ-associated genes (Mäki-Marttunen et al. 2017)
  293. Point process framework for modeling electrical stimulation of auditory nerve (Goldwyn et al. 2012)
  294. Population-level model of the basal ganglia and action selection (Gurney et al 2001, 2004)
  295. Prob. Inference of Short-Term Synaptic Plasticity in Neocort. Microcircuits (Costa et al. 2013)
  296. Purkinje neuron network (Zang et al. 2020)
  297. Pyramidal neurons with mutated SCN2A gene (Nav1.2) (Ben-Shalom et al 2017)
  298. Pyramidal neurons: IKHT offsets activation of IKLT to increase gain (Fernandez et al 2005)
  299. QIF method to estimate synaptic conductances (Vich et al 2017)
  300. Reaching movements with robust or stochastic optimal control models (Crevecoeur et al 2019)
  301. Realistic barrel cortical column - Matlab (Huang et al., 2022)
  302. Reconstrucing sleep dynamics with data assimilation (Sedigh-Sarvestani et al., 2012)
  303. Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011)
  304. Reflected SDE Hodgkin-Huxley Model (Dangerfield et al. 2012)
  305. Reichardt Model for Motion Detection in the Fly Visual System (Tuthill et al, 2011)
  306. Reinforcement Learning with Forgetting: Linking Sustained Dopamine to Motivation (Kato Morita 2016)
  307. Relative spike time coding and STDP-based orientation selectivity in V1 (Masquelier 2012)
  308. Reliability of Morris-Lecar neurons with added T, h, and AHP currents (Zeldenrust et al. 2013)
  309. Respiratory central pattern generator including Kolliker-Fuse nucleus (Wittman et al 2019)
  310. Respiratory control model with brainstem CPG and sensory feedback (Diekman, Thomas, and Wilson 2017)
  311. Respiratory control model with brainstem CPG and sensory feedback adapted for COVID-19 associated silent hypoxemia (Diekman et al., 2024)
  312. Response properties of neocort. neurons to temporally modulated noisy inputs (Koendgen et al. 2008)
  313. Resurgent Na+ current offers noise modulation in bursting neurons (Venugopal et al 2019)
  314. Reverse-time correlation analysis for idealized orientation tuning dynamics (Kovacic et al. 2008)
  315. Revised opponent-channel model of auditory space cortical representation (Briley & Summerfield 2013)
  316. Role of synchrony in sensation and the basis for paresthesia-free spinal cord stimulation (Sagalajev et al., 2024)
  317. Self-influencing synaptic plasticity (Tamosiunaite et al. 2007)
  318. Sequence learning via biophysically realistic learning rules (Cone and Shouval 2021)
  319. Sequential neuromodulation of Hebbian plasticity in reward-based navigation (Brzosko et al 2017)
  320. SHOT-CA3, RO-CA1 Training, & Simulation CODE in models of hippocampal replay (Nicola & Clopath 2019)
  321. Simple and accurate Diffusion Approximation algor. for stochastic ion channels (Orio & Soudry 2012)
  322. Simulating ion channel noise in an auditory brainstem neuron model (Schmerl & McDonnell 2013)
  323. Simulations of Reaching Adaptation and Control (Crevecoeur et al., 2022)
  324. Single E-I oscillating network with amplitude modulation (Avella Gonzalez et al. 2012)
  325. Single neuron with ion concentrations to model anoxic depolarization (Zandt et al. 2011)
  326. Single-cell comprehensive biophysical model of SN pars compacta (Muddapu & Chakravarthy 2021)
  327. Slow wave propagation in the guinea-pig gastric antrum (Hirst et al. 2006, Edwards and Hirst 2006)
  328. Smoothing of, and parameter estimation from, noisy biophysical recordings (Huys & Paninski 2009)
  329. Sound-evoked activity in peripheral axons of type I spiral ganglion neurons (Budak et al. 2021)
  330. Sparse connectivity is required for decorrelation, pattern separation (Cayco-Gajic et al 2017)
  331. Spatial coupling tunes NMDA receptor responses via Ca2+ diffusion (Iacobucci and Popescu 2019)
  332. Spatially-varying glutamate diffusion coefficient at CA1 synaptic cleft space (Gupta et al. 2016)
  333. Spectral method and high-order finite differences for nonlinear cable (Omurtag and Lytton 2010)
  334. Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation (Luque et al 2019)
  335. Spike frequency adaptation in the LGMD (Peron and Gabbiani 2009)
  336. Spike Response Model simulator (Jolivet et al. 2004, 2006, 2008)
  337. Spike timing detection in different forms of LTD (Doi et al 2005)
  338. Spiking GridPlaceMap model (Pilly & Grossberg, PLoS One, 2013)
  339. Spiking neuron model of the basal ganglia (Humphries et al 2006)
  340. Spinal circuits controlling limb coordination and gaits in quadrupeds (Danner et al 2017)
  341. State dependent drug binding to sodium channels in the dentate gyrus (Thomas & Petrou 2013)
  342. Statistical Long-term Synaptic Plasticity (statLTSP) (Costa et al 2017)
  343. Statistics of symmetry measure for networks of neurons (Esposito et al. 2014)
  344. STDP allows fast rate-modulated coding with Poisson-like spike trains (Gilson et al. 2011)
  345. Stochastic Hodgkin-Huxley Model: 14x28D Langevin Simulation (Pu and Thomas, 2020).
  346. Stochastic model for pituitary corticotrophs (Duncan et al., 2022)
  347. Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011)
  348. Stoney vs Histed: Quantifying spatial effects of intracortical microstims (Kumaravelu et al 2022)
  349. Strategy for kinase transport by microtubules to nerve terminals (Koon et al. 2014)
  350. Striatal dopamine ramping: an explanation by reinforcement learning with decay (Morita & Kato, 2014)
  351. Striatal GABAergic microcircuit, dopamine-modulated cell assemblies (Humphries et al. 2009)
  352. Striatal GABAergic microcircuit, spatial scales of dynamics (Humphries et al, 2010)
  353. Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013)
  354. Subiculum network model with dynamic chloride/potassium homeostasis (Buchin et al 2016)
  355. Subthreshold conductances regulate theta-frequency LFPs and spike phase (Sinha and Narayanan, 2015)
  356. Supervised learning in spiking neural networks with FORCE training (Nicola & Clopath 2017)
  357. Supervised learning with predictive coding (Whittington & Bogacz 2017)
  358. Surround Suppression in V1 via Withdraw of Balanced Local Excitation in V1 (Shushruth 2012)
  359. Switching circuit for optimal context integration during static + moving contexts (Voina et al 2022)
  360. Sympathetic neuron (Wheeler et al 2004)
  361. Sympathetic Preganglionic Neurone (Briant et al. 2014)
  362. Synaptic Impairment, Robustness of Excitatory NNs w/ Different Topologies (Mirzakhalili et al 2017)
  363. Synaptic plasticity can produce and enhance direction selectivity (Carver et al, 2008)
  364. Synchronized oscillations of clock gene expression in the choroid plexus (Myung et al 2018)
  365. Synthesis of spatial tuning functions from theta cell spike trains (Welday et al., 2011)
  366. Systems-level modeling of neuronal circuits for leech swimming (Zheng et al. 2007)
  367. Temporal and spatial characteristics of vibrissa responses to motor commands (Simony et al. 2010)
  368. Thalamic network model of deep brain stimulation in essential tremor (Birdno et al. 2012)
  369. Thalamic transformation of pallidal input (Hadipour-Niktarash 2006)
  370. Thalamo-cortical microcircuit (TCM) (AmirAli Farokhniaee and Madeleine M. Lowery 2021)
  371. The activity phase of postsynaptic neurons (Bose et al 2004)
  372. The role of network connectivity on epileptiform activity (Giacopelli et al 2021)
  373. The ventricular AP and effects of the isoproterenol-induced cardiac hypertrophy (Sengul et al 2020)
  374. Theoretical principles of DBS induced synaptic suppression (Farokhniaee & McIntyre 2019)
  375. Theta phase precession in a model CA3 place cell (Baker and Olds 2007)
  376. Towards a biologically plausible model of LGN-V1 pathways (Lian et al 2019)
  377. Transient and Steady-State Properties of Drosophila Sensory Neurons Coding Noxious Cold Temperature; (Maksymchuk, N., Sakurai, A., Cox, D. N., & Cymbalyuk, G. 2022)
  378. TTX-R Na+ current effect on cell response (Herzog et al 2001) (MATLAB)
  379. Understanding odor information segregation in the olfactory bulb by MC/TCs (Polese et al. 2014)
  380. V1 and AL spiking neural network for visual contrast response in mouse (Meijer et al. 2020)
  381. Vesicular pool simulations of synaptic depression (Aristizabal and Glavinovic 2004)
  382. Vestibulo-Ocular Reflex model in Matlab (Clopath at al. 2014)
  383. Voltage-based STDP synapse (Clopath et al. 2010)
  384. Wilson-Cowan Network with Homeostatic Plasticity (Nicola and Campbell 2021)
  385. Within movement adjustments of internal representations during reaching (Crevecoeur et al 2020)
  386. Working memory circuit with branched dendrites (Morita 2008)
  387. A cardiac cell simulator (Puglisi and Bers 2001), applied to the QT interval (Busjahn et al 2004)
  388. A comparison of mathematical models of mood in bipolar disorder (Cochran et al. 2017)
  389. A CORF computational model of a simple cell that relies on LGN input (Azzopardi & Petkov 2012)
  390. A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013)
  391. A dynamic model of the canine ventricular myocyte (Hund, Rudy 2004)
  392. A gap junction network of Amacrine Cells controls Nitric Oxide release (Jacoby et al 2018)
  393. A model for focal seizure onset, propagation, evolution, and progression (Liou et al 2020)
  394. A neural mass model for critical assessment of brain connectivity (Ursino et al 2020)
  395. A neural mass model of cross frequency coupling (Chehelcheraghi et al 2017)
  396. A neurocomputational model of classical conditioning phenomena (Moustafa et al. 2009)
  397. A reinforcement learning example (Sutton and Barto 1998)
  398. A simple integrative electrophysiological model of bursting GnRH neurons (Csercsik et al. 2011)
  399. Activity constraints on stable neuronal or network parameters (Olypher and Calabrese 2007)
  400. Analyzing neural time series data theory and practice (Cohen 2014)
  401. Auditory nerve spontaneous rate histograms (Jackson and Carney 2005)
  402. Binocular energy model set for binocular neurons in optic lobe of praying mantis (Rosner et al 2019)
  403. Brain Dynamics Toolbox (Heitmann & Breakspear 2016, 2017, 2018)
  404. Cat auditory nerve model (Zilany and Bruce 2006, 2007)
  405. Cerebellar stellate cells: changes in threshold, latency and frequency of firing (Mitry et al 2020)
  406. Cochlear implant models (Bruce et al. 1999a, b, c, 2000)
  407. Continuous lateral oscillations as a mechanism for taxis in Drosophila larvae (Wystrach et al 2016)
  408. Disrupted information processing in Fmr1-KO mouse layer 4 barrel cortex (Domanski et al 2019)
  409. Dynamics of sleep oscillations coupled to brain temperature on multiple scales (Csernai et al 2019)
  410. DynaSim: a MATLAB toolbox for neural modeling and simulation (Sherfey et al 2018)
  411. Evaluation of stochastic diff. eq. approximation of ion channel gating models (Bruce 2009)
  412. Fixed point attractor (Hasselmo et al 1995)
  413. Gamma and theta rythms in biophysical models of hippocampus circuits (Kopell et al. 2011)
  414. Generating coherent patterns of activity from chaotic neural networks (Sussillo and Abbott 2009)
  415. High-Res. Recordings Using a Real-Time Computational Model of the Electrode (Brette et al. 2008)
  416. Hippocampal context-dependent retrieval (Hasselmo and Eichenbaum 2005)
  417. Hodgkin–Huxley model with fractional gating (Teka et al. 2016)
  418. Human seizures couple across spatial scales through travelling wave dynamics (Martinet et al 2017)
  419. Implementation issues in approximate methods for stochastic Hodgkin-Huxley models (Bruce 2007)
  420. Inhibitory cells enable sparse coding in V1 model (King et al. 2013)
  421. Integrate and fire model code for spike-based coincidence-detection (Heinz et al. 2001, others)
  422. Levodopa-Induced Toxicity in Parkinson's Disease (Muddapu et al, 2022)
  423. Logarithmic distributions prove that intrinsic learning is Hebbian (Scheler 2017)
  424. Long-term adaptation with power-law dynamics (Zilany et al. 2009)
  425. Loss of phase-locking in non-weakly coupled inhib. networks of type-I neurons (Oh and Matveev 2009)
  426. Mathematics for Neuroscientists (Gabbiani and Cox 2010)
  427. MATLAB for brain and cognitive scientists (Cohen 2017)
  428. Mature and young adult-born dentate granule cell models (T2N interface) (Beining et al. 2017)
  429. Method for counting motor units in mice (Major et al 2007)
  430. Method of probabilistic principle surfaces (PPS) (Chang and Ghosh 2001)
  431. Microglial cytokine network (Anderson et al., 2015)
  432. Model of generalized periodic discharges in acute hepatic encephalopathy (Song et al 2019)
  433. Model of neural responses to amplitude-modulated tones (Nelson and Carney 2004)
  434. Modeling conductivity profiles in the deep neocortical pyramidal neuron (Wang K et al. 2013)
  435. Models analysis for auditory-nerve synapse (Zhang and Carney 2005)
  436. Models for diotic and dichotic detection (Davidson et al. 2009)
  437. Multi-timescale adaptive threshold model (Kobayashi et al 2009)
  438. Multiscale model of excitotoxicity in PD (Muddapu and Chakravarthy 2020)
  439. Multistability of clustered states in a globally inhibitory network (Chandrasekaran et al. 2009)
  440. Network topologies for producing limited sustained activation (Kaiser and Hilgetag 2010)
  441. Neural field model to reconcile structure with function in V1 (Rankin & Chavane 2017)
  442. Neural Mass Model for relationship between Brain Rhythms + Functional Connectivity (Ricci et al '21)
  443. Neural mass model of spindle generation in the isolated thalamus (Schellenberger Costa et al. 2016)
  444. Neural mass model of the neocortex under sleep regulation (Costa et al 2016)
  445. Neural mass model of the sleeping thalamocortical system (Schellenberger Costa et al 2016)
  446. Neural model of two-interval discrimination (Machens et al 2005)
  447. Neural recruitment during synchronous multichannel microstimulation (Hokanson et al 2018)
  448. NeuroManager: a workflow analysis based simulation management engine (Stockton & Santamaria 2015)
  449. NN for proto-object based contour integration and figure-ground segregation (Hu & Niebur 2017)
  450. Nodose sensory neuron (Schild et al. 1994, Schild and Kunze 1997)
  451. Nonlinear neuronal computation based on physiologically plausible inputs (McFarland et al. 2013)
  452. Phase-locking analysis with transcranial magneto-acoustical stimulation (Yuan et al 2017)
  453. Polychronization: Computation With Spikes (Izhikevich 2005)
  454. Prefrontal cortical mechanisms for goal-directed behavior (Hasselmo 2005)
  455. Prefrontal–striatal Parkinsons comp. model of multicue category learning (Moustafa and Gluck 2011)
  456. Quantitative assessment of computational models for retinotopic map formation (Hjorth et al. 2015)
  457. Reduction of nonlinear ODE systems possessing multiple scales (Clewley et al. 2005)
  458. Response properties of an integrate and fire model (Zhang and Carney 2005)
  459. Role of KCNQ1 and IKs in cardiac repolarization (Silva, Rudy 2005)
  460. Single-cell comprehensive biophysical model of SN pars compacta (Muddapu & Chakravarthy 2021)
  461. Squid axon (Hodgkin, Huxley 1952) (LabAXON)
  462. Stimulated and physiologically induced APs: frequency and fiber diameter (Sadashivaiah et al 2018)
  463. Sympathetic neuron (Wheeler et al 2004)
  464. Synaptic damage underlies EEG abnormalities in postanoxic encephalopathy (Ruijter et al 2017)
  465. Synaptic strengths are critical in creating the proper output phasing in a CPG (Gunay et al 2019)
  466. The dynamics underlying pseudo-plateau bursting in a pituitary cell model (Teka et al. 2011)
  467. Two-cell inhibitory network bursting dynamics captured in a one-dimensional map (Matveev et al 2007)
  468. Voltage and light-sensitive Channelrhodopsin-2 model (ChR2) (Williams et al. 2013)
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