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Integrated Models is a virtual database currently indexing computational models from: CellML, ModelDB, Open Source Brain, SimTK.
(last updated: Nov 23, 2022)
Data or Model Models| Database | Model Name | Simulator Software | Model Type | Neurons | Neurotransmitters | Receptors | ||||
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ModelDB | Sleep-wake transitions in corticothalamic system (Bazhenov et al 2002) | C or C++ program | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex L5/6 pyramidal GLU cell | GabaA, GabaB, AMPA, NMDA | I Na,t, I L high threshold, I T low threshold, I K,leak, I M, I K,Ca | Depression, Oscillations, Synchronization, Spatio-temporal Activity Patterns, Short-term Synaptic Plasticity, Sleep | The authors investigate the transition between sleep and awake states with intracellular recordings in cats and computational models. The model describes many essential features of slow wave sleep and activated states as well as the transition between them. | Bazhenov, Maxim [Bazhenov at Salk.edu] | |
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ModelDB | Thalamic Reticular Network (Destexhe et al 1994) | NEURON | Realistic Network | Thalamus reticular nucleus GABA cell | GabaA, GabaB | I T low threshold, I K,Ca, I CAN | Activity Patterns, Temporal Pattern Generation, Oscillations, Tutorial/Teaching, Sleep, Calcium dynamics, Spindles | Demo for simulating networks of thalamic reticular neurons (reproduces figures from Destexhe A et al 1994) | Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr] | |
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ModelDB | Thalamocortical and Thalamic Reticular Network (Destexhe et al 1996) | NEURON | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | GabaA, GabaB, AMPA | I Na,t, I T low threshold, I K,leak, I h | Activity Patterns, Oscillations, Synchronization, Spatio-temporal Activity Patterns, Sleep, Calcium dynamics, Spindles | NEURON model of oscillations in networks of thalamocortical and thalamic reticular neurons in the ferret. (more applications for a model quantitatively identical to previous DLGN model; updated for NEURON v4 and above) | Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr] | |
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ModelDB | Neural mass model of the sleeping thalamocortical system (Schellenberger Costa et al 2016) | Network, C or C++ program (web link to model), MATLAB (web link to model) | Neural mass | Neocortex L2/3 pyramidal GLU cell, Thalamus reticular nucleus GABA cell, Thalamus geniculate nucleus/lateral principal GLU cell, Neocortex U1 L6 pyramidal corticalthalamic GLU cell | AMPA, Gaba, NMDA | I Calcium, Na/K pump, I_K,Na | Calcium dynamics, Sleep, Activity Patterns, Oscillations, Bifurcation, Spindles, Audition | This paper generates typical human EEG data of sleep stages N2/N3 as well as wakefulness and REM sleep. | Schellenberger Costa, Michael [mschellenbergercosta at gmail.com] | |
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ModelDB | Electrodecrements in in vitro model of infantile spasms (Traub et al 2020) | FORTRAN | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex U1 L6 pyramidal corticalthalamic GLU cell, Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell | I Na,p, I Na,t, I L high threshold, I A, I K, I M, I h, I K,Ca, I Calcium, I A, slow | Brain Rhythms, Epilepsy | The code is an extension of the thalamocortical model of Traub et al. (2005) J Neurophysiol. It is here applied to an in vitro model of the electrodecremental response seen in the EEG of children with infantile spasms (West syndrome) | Traub, Roger D [rtraub at us.ibm.com] | ||
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ModelDB | Pyramidal Neuron: Deep, Thalamic Relay and Reticular, Interneuron (Destexhe et al 1998, 2001) | NEURON | Neuron or other electrically excitable cell | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex L5/6 pyramidal GLU cell | GabaA, GabaB, AMPA, Gaba | I Sodium, I Calcium, I Potassium, I Na,t, I T low threshold, I K, I M | Activity Patterns, Bursting, Action Potentials, Calcium dynamics | This package shows single-compartment models of different classes of cortical neurons, such as the "regular-spiking", "fast-spiking" and "bursting" (LTS) neurons. The mechanisms included are the Na+ and K+ currents for generating action potentials (INa, IKd), the T-type calcium current (ICaT), and a slow voltage-dependent K+ current (IM). See http://cns.fmed.ulaval.ca/alain_demos.html | Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr] | |
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ModelDB | Thalamic quiescence of spike and wave seizures (Lytton et al 1997) | NEURON | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | Gaba, Glutamate | GabaA, Glutamate | I T low threshold | Temporal Pattern Generation, Oscillations, Calcium dynamics | A phase plane analysis of a two cell interaction between a thalamocortical neuron (TC) and a thalamic reticularis neuron (RE). | Lytton, William [bill.lytton at downstate.edu], Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr] |
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ModelDB | Computer model of clonazepam`s effect in thalamic slice (Lytton 1997) | NEURON | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | Gaba | GabaA, Gaba | I Na,t, I T low threshold, I K, I CAN | Therapeutics, Activity Patterns, Bursting, Epilepsy, Calcium dynamics | Demonstration of the effect of a minor pharmacological synaptic change at the network level. Clonazepam, a benzodiazepine, enhances inhibition but is paradoxically useful for certain types of seizures. This simulation shows how inhibition of inhibitory cells (the RE cells) produces this counter-intuitive effect. | Lytton, William [bill.lytton at downstate.edu] |
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ModelDB | Thalamic reticular neurons: the role of Ca currents (Destexhe et al 1996) | NEURON | Neuron or other electrically excitable cell | Thalamus reticular nucleus GABA cell | I Sodium, I Calcium, I Potassium, I Na,t, I T low threshold, I K | Action Potential Initiation, Dendritic Action Potentials, Bursting, Simplified Models, Active Dendrites, Influence of Dendritic Geometry, Detailed Neuronal Models, Action Potentials, Calcium dynamics | The experiments and modeling reported in this paper show how intrinsic bursting properties of RE cells may be explained by dendritic calcium currents. | Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr] | ||
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ModelDB | Thalamocortical augmenting response (Bazhenov et al 1998) | NEURON | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex L5/6 pyramidal GLU cell | Gaba, Glutamate | GabaA, GabaB, AMPA | I Na,t, I T low threshold, I A, I K,Ca | Synchronization, Synaptic Integration | In the cortical model, augmenting responses were more powerful in the "input" layer compared with those in the "output" layer. Cortical stimulation of the network model produced augmenting responses in cortical neurons in distant cortical areas through corticothalamocortical loops and low-threshold intrathalamic augmentation. ... The predictions of the model were compared with in vivo recordings from neurons in cortical area 4 and thalamic ventrolateral nucleus of anesthetized cats. The known intrinsic properties of thalamic cells and thalamocortical interconnections can account for the basic properties of cortical augmenting responses. See reference for details. NEURON implementation note: cortical SU cells are getting slightly too little stimulation - reason unknown. | Lytton, William [bill.lytton at downstate.edu] |
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ModelDB | A single column thalamocortical network model (Traub et al 2005) | NEURON, FORTRAN | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex U1 L6 pyramidal corticalthalamic GLU cell, Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell | GabaA, AMPA, NMDA | I Na,p, I Na,t, I L high threshold, I T low threshold, I A, I K, I M, I h, I K,Ca, I Calcium, I A, slow | Activity Patterns, Bursting, Temporal Pattern Generation, Oscillations, Simplified Models, Epilepsy, Sleep, Spindles | To better understand population phenomena in thalamocortical neuronal ensembles, we have constructed a preliminary network model with 3,560 multicompartment neurons (containing soma, branching dendrites, and a portion of axon). Types of neurons included superficial pyramids (with regular spiking [RS] and fast rhythmic bursting [FRB] firing behaviors); RS spiny stellates; fast spiking (FS) interneurons, with basket-type and axoaxonic types of connectivity, and located in superficial and deep cortical layers; low threshold spiking (LTS) interneurons, that contacted principal cell dendrites; deep pyramids, that could have RS or intrinsic bursting (IB) firing behaviors, and endowed either with non-tufted apical dendrites or with long tufted apical dendrites; thalamocortical relay (TCR) cells; and nucleus reticularis (nRT) cells. To the extent possible, both electrophysiology and synaptic connectivity were based on published data, although many arbitrary choices were necessary. | Traub, Roger D [rtraub at us.ibm.com] | |
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ModelDB | Coding of stimulus frequency by latency in thalamic networks (Golomb et al 2005) | C or C++ program | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | Gaba, Glutamate | GabaA, GabaB, AMPA | Simplified Models, Rate-coding model neurons | The paper presents models of the rat vibrissa processing system including the posterior medial (POm) thalamus, ventroposterior medial (VPm) thalamus, and GABAB- mediated feedback inhibition from the reticular thalamic (Rt) nucleus. A clear match between the experimentally measured spike-rates and the numerically calculated rates for the full model occurs when VPm thalamus receives stronger brainstem input and weaker GABAB-mediated inhibition than POm thalamus. | Golomb, David [golomb at bgu.ac.il] | |
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ModelDB | Thalamic transformation of pallidal input (Hadipour-Niktarash 2006) | MATLAB | Realistic Network, Neuron or other electrically excitable cell | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | GabaA, GabaB, AMPA | I Potassium, I Na,t, I T low threshold, I K, I h | Parkinson's | "In Parkinson’s disease, neurons of the internal segment of the globus pallidus (GPi) display the low-frequency tremor-related oscillations. These oscillatory activities are transmitted to the thalamic relay nuclei. Computer models of the interacting thalamocortical (TC) and thalamic reticular (RE) neurons were used to explore how the TC-RE network processes the low-frequency oscillations of the GPi neurons. ..." | Hadipour-Niktarash, Arash [arash.hadipour at gmail.com] | |
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ModelDB | Spikes,synchrony,and attentive learning by laminar thalamocort. circuits (Grossberg & Versace 2007) | NeuroML (web link to model), KInNeSS (web link to model), XML (web link to model) | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex L5/6 pyramidal GLU cell, Neocortex L2/3 pyramidal GLU cell | AMPA, Gaba, Cholinergic Receptors | I Potassium, I Na,t, I T low threshold, I K | Spatial Navigation, Pattern Recognition, Activity Patterns, Oscillations, Synchronization, Working memory, STDP | "... The model hereby clarifies, for the first time, how the following levels of brain organization coexist to realize cognitive processing properties that regulate fast learning and stable memory of brain representations: single cell properties, such as spiking dynamics, spike-timing-dependent plasticity (STDP), and acetylcholine modulation; detailed laminar thalamic and cortical circuit designs and their interactions; aggregate cell recordings, such as current-source densities and local field potentials; and single cell and large-scale inter-areal oscillations in the gamma and beta frequency domains. ..." | ||
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ModelDB | A contracting model of the basal ganglia (Girard et al. 2008) | Python | Realistic Network | Neostriatum medium spiny direct pathway GABA cell, Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | Dopamine | D1, D2 | Action Selection/Decision Making | Basal ganglia model : selection processes between channels, dynamics controlled by contraction analysis, rate-coding model of neurons based on locally projected dynamical systems (lPDS). | Girard, Benoit [girard at isir.upmc.fr] | |
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ModelDB | A Model Circuit of Thalamocortical Convergence (Behuret et al. 2013) | NEURON | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex U1 L5B pyramidal pyramidal tract GLU cell, Retina ganglion GLU cell | GabaA, AMPA | I Na,t, I T low threshold, I K, I M | Synaptic Convergence | “… Using dynamic-clamp techniques in thalamic slices in vitro, we combined theoretical and experimental approaches to implement a realistic hybrid retino-thalamo-cortical pathway mixing biological cells and simulated circuits. … The study of the impact of the simulated cortical input on the global retinocortical signal transfer efficiency revealed a novel control mechanism resulting from the collective resonance of all thalamic relay neurons. We show here that the transfer efficiency of sensory input transmission depends on three key features: i) the number of thalamocortical cells involved in the many-to-one convergence from thalamus to cortex, ii) the statistics of the corticothalamic synaptic bombardment and iii) the level of correlation imposed between converging thalamic relay cells. In particular, our results demonstrate counterintuitively that the retinocortical signal transfer efficiency increases when the level of correlation across thalamic cells decreases. …” | Behuret, Sebastien [behuret at unic.cnrs-gif.fr] | |
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ModelDB | Neural mass model of spindle generation in the isolated thalamus (Schellenberger Costa et al. 2016) | Network, C or C++ program (web link to model), MATLAB (web link to model) | Neural mass | Thalamus reticular nucleus GABA cell, Thalamus geniculate nucleus/lateral principal GLU cell | Gaba, AMPA, NMDA | I K,Ca, I Calcium | Calcium dynamics, Sleep, Activity Patterns, Oscillations, Bifurcation, Spindles, Audition | The model generates different oscillatory patterns in the thalamus, including delta and spindle band oscillations. | Schellenberger Costa, Michael [mschellenbergercosta at gmail.com] | |
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ModelDB | A multilayer cortical model to study seizure propagation across microdomains (Basu et al. 2015) | GENESIS | Realistic Network | Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell, Neocortex U1 L5B pyramidal pyramidal tract GLU cell, Thalamus reticular nucleus GABA cell | Glutamate, Gaba, Amino Acids | AMPA, GabaA, NMDA | I Na,p, I Na,t, I K, I A, I M, I h, I K,Ca, I A, slow, I L high threshold, I T low threshold, I Calcium | Activity Patterns, Epilepsy | A realistic neural network was used to simulate a region of neocortex to obtain extracellular LFPs from ‘virtual micro-electrodes’ and produce test data for comparison with multisite microelectrode recordings. A model was implemented in the GENESIS neurosimulator. A simulated region of cortex was represented by layers 2/3, 5/6 (interneurons and pyramidal cells) and layer 4 stelate cells, spaced at 25 µm in each horizontal direction. Pyramidal cells received AMPA and NMDA inputs from neighboring cells at the basal and apical dendrites. The LFP data was generated by simulating 16-site electrode array with the help of ‘efield’ objects arranged at the predetermined positions with respect to the surface of the simulated network. The LFP for the model is derived from a weighted average of the current sources summed over all cellular compartments. Cell models were taken from from Traub et al. (2005) J Neurophysiol 93(4):2194-232. | Anderson, WS, Kudela, Pawel |
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ModelDB | Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) | NEURON (web link to model), Python (web link to model) | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell, Neocortex L5/6 pyramidal GLU cell, Neocortex L2/3 pyramidal GLU cell, Neocortex V1 L5B pyramidal pyramidal tract GLU cell | GabaA, AMPA, NMDA | I Na,p, I Na,t, I L high threshold, I T low threshold, I A, I K, I M, I h, I K,Ca, I Calcium, I A, slow | Activity Patterns, Bursting, Temporal Pattern Generation, Oscillations, Simplified Models, Epilepsy, Sleep, Methods, Spindles | "A major challenge in experimental data analysis is the validation of analytical methods in a fully controlled scenario where the justification of the interpretation can be made directly and not just by plausibility. ... One solution is to use simulations of realistic models to generate ground truth data. In neuroscience, creating such data requires plausible models of neural activity, access to high performance computers, expertise and time to prepare and run the simulations, and to process the output. To facilitate such validation tests of analytical methods we provide rich data sets including intracellular voltage traces, transmembrane currents, morphologies, and spike times. ... The data were generated using the largest publicly available multicompartmental model of thalamocortical network (Traub et al. 2005), with activity evoked by different thalamic stimuli." | Glabska, Helena [glabska@gmail.com [glabska at gmail.com], Chintaluri, Chaitanya [c.chintaluri at nencki.gov.pl] | |
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ModelDB | A unified thalamic model of multiple distinct oscillations (Li, Henriquez and Fröhlich 2017) | C or C++ program | Realistic Network | Thalamus geniculate nucleus/lateral principal GLU cell, Thalamus reticular nucleus GABA cell | Acetylcholine, Norephinephrine | AMPA, NMDA, GabaA | I Na,t, I K, I h, I L high threshold, I T low threshold, I_AHP, I CAN, I K,leak | Sleep, Activity Patterns, Gamma oscillations, Oscillations, Brain Rhythms | We present a unified model of the thalamus that is capable of independently generating multiple distinct oscillations (delta, spindle, alpha and gamma oscillations) under different levels of acetylcholine (ACh) and norepinephrine (NE) modulation corresponding to different physiological conditions (deep sleep, light sleep, relaxed wakefulness and attention). The model also shows that entrainment of thalamic oscillations is state-dependent. | Li, Guoshi [guoshi_li at med.unc.edu] |
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