ModelDB
ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models.
Description
More detailed information about this field from each metasource.
ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models.
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. The model source code doesn't even have to reside inside ModelDB; it just has to be available from some publicly accessible online repository or WWW site.
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
Webpage:
http://senselab.med.yale.edu/modeldbWebpage
More detailed information about this field from each metasource.
http://senselab.med.yale.edu/modeldb
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://senselab.med.yale.edu/ModelDB/default.cshtml
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
Licence:
Name: otherLicence name
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other
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
Licence URL
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https://www.gnu.org/licenses/
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
ModelDB: A Database to Support Computational Neuroscience
PMID: 15218350
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
PMID: 27629590
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ModelDB: making models publicly accessible to support computational neuroscience
PMID: 15055399
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ModelDB: an environment for running and storing computational models and their results applied to neuroscience
PMID: 8930855
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
ModelDB: A Database to Support Computational Neuroscience
PMID: 15218350
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
PMID: 27629590
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ModelDB: making models publicly accessible to support computational neuroscience
PMID: 15055399
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ModelDB: an environment for running and storing computational models and their results applied to neuroscience
PMID: 8930855
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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ModelDB: A Database to Support Computational Neuroscience
PubMed citations: 175.
175 articles citing: ModelDB: A Database to Support Computational Neuroscience
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models. PMID:35784184
Phase coding of spatial representations in the human entorhinal cortex. PMID:35507662
Modeling Dendrites and Spatially-Distributed Neuronal Membrane Properties. PMID:35471534
Dendritic synapse geometry optimizes binaural computation in a sound localization circuit. PMID:34818046
Corticothalamic Pathways From Layer 5: Emerging Roles in Computation and Pathology. PMID:34566583
Active Dendrites and Local Field Potentials: Biophysical Mechanisms and Computational Explorations. PMID:34506834
NetPyNE Implementation and Scaling of the Potjans-Diesmann Cortical Microcircuit Model. PMID:34411272
Event-Based Update of Synapses in Voltage-Based Learning Rules. PMID:34177505
Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era. PMID:33616035
A Minimal Biophysical Model of Neocortical Pyramidal Cells: Implications for Frontal Cortex Microcircuitry and Field Potential Generation. PMID:33037076
Challenges in Physiological Phenotyping of hiPSC-Derived Neurons: From 2D Cultures to 3D Brain Organoids. PMID:32984317
Excitatory-Inhibitory Synaptic Coupling in Avian Nucleus Magnocellularis. PMID:31727796
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Curated Model Development Using NEUROiD: A Web-Based NEUROmotor Integration and Design Platform. PMID:31440153
Energy-efficient information transfer at thalamocortical synapses. PMID:31381555
Degeneracy in hippocampal physiology and plasticity. PMID:31301166
Feedforward Thalamocortical Connectivity Preserves Stimulus Timing Information in Sensory Pathways. PMID:31270157
Dramatically Amplified Thoracic Sympathetic Postganglionic Excitability and Integrative Capacity Revealed with Whole-Cell Patch-Clamp Recordings. PMID:31040159
PaperBot: open-source web-based search and metadata organization of scientific literature. PMID:30678631
Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization. PMID:30483089
Optimal Localist and Distributed Coding of Spatiotemporal Spike Patterns Through STDP and Coincidence Detection. PMID:30279653
Disentangling astroglial physiology with a realistic cell model in silico. PMID:30177844
Effects of Synchronous Electrode Pulses on Neural Recruitment During Multichannel Microstimulation. PMID:30166583
Differential changes to D1 and D2 medium spiny neurons in the 12-month-old Q175+/- mouse model of Huntington's Disease. PMID:30118496
NDDN: A Cloud-Based Neuroinformation Database for Developing Neuronal Networks. PMID:30073046
BioNet: A Python interface to NEURON for modeling large-scale networks. PMID:30071069
h-Type Membrane Current Shapes the Local Field Potential from Populations of Pyramidal Neurons. PMID:29875266
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Modeling sources of interlaboratory variability in electrophysiological properties of mammalian neurons. PMID:29357465
Supervised learning in spiking neural networks with FORCE training. PMID:29263361
Diversity of Evoked Astrocyte Ca2+ Dynamics Quantified through Experimental Measurements and Mathematical Modeling. PMID:29109680
The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization. PMID:29023523
The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study. PMID:28970791
Computational analysis of network activity and spatial reach of sharp wave-ripples. PMID:28915251
Dipolar extracellular potentials generated by axonal projections. PMID:28871959
Software for Brain Network Simulations: A Comparative Study. PMID:28775687
The effects of paranodal myelin damage on action potential depend on axonal structure. PMID:28770425
A consensus layer V pyramidal neuron can sustain interpulse-interval coding. PMID:28704450
STDP Allows Close-to-Optimal Spatiotemporal Spike Pattern Detection by Single Coincidence Detector Neurons. PMID:28668487
Intraglomerular gap junctions enhance interglomerular synchrony in a sparsely connected olfactory bulb network. PMID:28640508
Toward standard practices for sharing computer code and programs in neuroscience. PMID:28542156
The basis of sharp spike onset in standard biophysical models. PMID:28441389
Context-dependent spatially periodic activity in the human entorhinal cortex. PMID:28396399
Mathematical investigation of IP3-dependent calcium dynamics in astrocytes. PMID:28353176
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
Mapping the function of neuronal ion channels in model and experiment. PMID:28267430
Dendritic trafficking faces physiologically critical speed-precision tradeoffs. PMID:28034367
Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb. PMID:28005923
Internal Cholinergic Regulation of Learning and Recall in a Model of Olfactory Processing. PMID:27877112
Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks. PMID:27797828
Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. PMID:27760819
Using a Semi-Automated Strategy to Develop Multi-Compartment Models That Predict Biophysical Properties of Interneuron-Specific 3 (IS3) Cells in Hippocampus. PMID:27679813
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. PMID:27629590
Is realistic neuronal modeling realistic? PMID:27535372
Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim. PMID:27445781
N3DFix: an Algorithm for Automatic Removal of Swelling Artifacts in Neuronal Reconstructions. PMID:27412029
Functionalized anatomical models for EM-neuron Interaction modeling. PMID:27224508
Investigation of assumptions underlying current safety guidelines on EM-induced nerve stimulation. PMID:27223274
Biophysical Network Modelling of the dLGN Circuit: Different Effects of Triadic and Axonal Inhibition on Visual Responses of Relay Cells. PMID:27203421
A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. PMID:27148027
Granule cell excitability regulates gamma and beta oscillations in a model of the olfactory bulb dendrodendritic microcircuit. PMID:27121582
Active subthreshold dendritic conductances shape the local field potential. PMID:27079755
Microsaccades enable efficient synchrony-based coding in the retina: a simulation study. PMID:27063867
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
Anions Govern Cell Volume: A Case Study of Relative Astrocytic and Neuronal Swelling in Spreading Depolarization. PMID:26974767
A general homeostatic principle following lesion induced dendritic remodeling. PMID:26916562
Large extracellular space leads to neuronal susceptibility to ischemic injury in a Na+/K+ pumps-dependent manner. PMID:26852334
Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain. PMID:26751378
Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells. PMID:26674618
Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes. PMID:26621106
Redistribution of Kv1 and Kv7 enhances neuronal excitability during structural axon initial segment plasticity. PMID:26581625
NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. PMID:26528175
Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features. PMID:26491963
Effects of Neural Morphology and Input Distribution on Synaptic Processing by Global and Focal NMDA-Spikes. PMID:26460829
Computational modeling of cytokine signaling in microglia. PMID:26440115
3D-printer visualization of neuron models. PMID:26175684
Network Mechanisms Generating Abnormal and Normal Hippocampal High-Frequency Oscillations: A Computational Analysis. PMID:26146658
Computational modeling suggests distinct, location-specific function of norepinephrine in olfactory bulb and piriform cortex. PMID:26136678
A Million-Plus Neuron Model of the Hippocampal Dentate Gyrus: Critical Role for Topography in Determining Spatiotemporal Network Dynamics. PMID:26087482
Collaborating and sharing data in epilepsy research. PMID:26035676
Simulation of alcohol action upon a detailed Purkinje neuron model and a simpler surrogate model that runs >400 times faster. PMID:25928094
On the firing rate dependency of the phase response curve of rat Purkinje neurons in vitro. PMID:25775448
Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. PMID:25734493
Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb. PMID:25717156
Control of sleep-to-wake transitions via fast aminoacid and slow neuropeptide transmission. PMID:25598695
Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology. PMID:25564868
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Functional consequences of age-related morphologic changes to pyramidal neurons of the rhesus monkey prefrontal cortex. PMID:25527184
Linking macroscopic with microscopic neuroanatomy using synthetic neuronal populations. PMID:25340814
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. PMID:25205662
Distinct roles of bulbar muscarinic and nicotinic receptors in olfactory discrimination learning. PMID:25143606
A neural mass model based on single cell dynamics to model pathophysiology. PMID:25131270
Cannabinoid-mediated short-term plasticity in hippocampus. PMID:25123173
Increased intrinsic excitability of muscle vasoconstrictor preganglionic neurons may contribute to the elevated sympathetic activity in hypertensive rats. PMID:25122704
ModelDB in computational neuroscience education - a research tool as interactive educational media. PMID:25089156
Contribution of PKC to the maintenance of 5-HT-induced short-term facilitation at sensorimotor synapses of Aplysia. PMID:25031258
Measuring symmetry, asymmetry and randomness in neural network connectivity. PMID:25006663
Dendrites impact the encoding capabilities of the axon. PMID:24920612
NeuroElectro: a window to the world's neuron electrophysiology data. PMID:24808858
Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity. PMID:24659956
A unifying theory of synaptic long-term plasticity based on a sparse distribution of synaptic strength. PMID:24624080
Modeling intracellular signaling underlying striatal function in health and disease. PMID:24560149
morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python. PMID:24478690
LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons. PMID:24474916
Emergence of connectivity motifs in networks of model neurons with short- and long-term plastic synapses. PMID:24454735
Distinguishing mechanisms of gamma frequency oscillations in human current source signals using a computational model of a laminar neocortical network. PMID:24385958
A computational model for epidural electrical stimulation of spinal sensorimotor circuits. PMID:24305828
Network bursting dynamics in excitatory cortical neuron cultures results from the combination of different adaptive mechanisms. PMID:24146781
Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. PMID:23678009
A biophysical model of endocannabinoid-mediated short term depression in hippocampal inhibition. PMID:23527052
The energy cost of action potential propagation in dopamine neurons: clues to susceptibility in Parkinson's disease. PMID:23515615
A new method to infer higher-order spike correlations from membrane potentials. PMID:23474914
The cooperation of sustained and phasic inhibitions increases the contrast of ITD-tuning in low-frequency neurons of the chick nucleus laminaris. PMID:23447603
Bifurcations of large networks of two-dimensional integrate and fire neurons. PMID:23430291
The periglomerular cell of the olfactory bulb and its role in controlling mitral cell spiking: a computational model. PMID:23405261
Fast computations in cortical ensembles require rapid initiation of action potentials. PMID:23392659
A model of cholinergic modulation in olfactory bulb and piriform cortex. PMID:23221406
A mechanism for robust circadian timekeeping via stoichiometric balance. PMID:23212247
Cortical dendritic spine heads are not electrically isolated by the spine neck from membrane potential signals in parent dendrites. PMID:23054810
Influence of highly distinctive structural properties on the excitability of pyramidal neurons in monkey visual and prefrontal cortices. PMID:23035077
Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. PMID:22685429
A tool for multi-scale modelling of the renal nephron. PMID:22670210
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Strength-duration relationship for intra- versus extracellular stimulation with microelectrodes. PMID:22516015
Mitral cell spike synchrony modulated by dendrodendritic synapse location. PMID:22319487
A federated design for a neurobiological simulation engine: the CBI federated software architecture. PMID:22242154
Channelpedia: an integrative and interactive database for ion channels. PMID:22232598
Phase precession through acceleration of local theta rhythm: a biophysical model for the interaction between place cells and local inhibitory neurons. PMID:22215520
The what and where of adding channel noise to the Hodgkin-Huxley equations. PMID:22125479
Cosine directional tuning of theta cell burst frequencies: evidence for spatial coding by oscillatory interference. PMID:22072668
Chloride ions in the pore of glycine and GABA channels shape the time course and voltage dependence of agonist currents. PMID:21976494
Computational modeling of epilepsy. PMID:21967351
Properties and functional implications of I (h) in hippocampal area CA3 interneurons. PMID:21938402
Hyperconnectivity and slow synapses during early development of medial prefrontal cortex in a mouse model for mental retardation and autism. PMID:21856714
Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PMID:21829333
Neural dynamics during anoxia and the "wave of death". PMID:21779384
Democratic population decisions result in robust policy-gradient learning: a parametric study with GPU simulations. PMID:21572529
Imperfect space clamp permits electrotonic interactions between inhibitory and excitatory synaptic conductances, distorting voltage clamp recordings. PMID:21559357
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models. PMID:21559300
Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation. PMID:21423712
Inverse current source density method in two dimensions: inferring neural activation from multielectrode recordings. PMID:21409556
Network recruitment to coherent oscillations in a hippocampal computer model. PMID:21273309
A computer model of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. PMID:21191641
Postsynaptic signal transduction models for long-term potentiation and depression. PMID:21188161
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PMID:20585541
Multivariate autoregressive modeling and granger causality analysis of multiple spike trains. PMID:20454705
Computational modeling of GABAA receptor-mediated paired-pulse inhibition in the dentate gyrus. PMID:20177763
Neuroinformatics: from bioinformatics to databasing the brain. PMID:19812780
Role of A-type potassium currents in excitability, network synchronicity, and epilepsy. PMID:19777555
Towards reproducible descriptions of neuronal network models. PMID:19662159
Establishing a novel modeling tool: a python-based interface for a neuromorphic hardware system. PMID:19562085
PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python. PMID:19543450
Database analysis of simulated and recorded electrophysiological datasets with PANDORA's toolbox. PMID:19475520
Smoothing of, and parameter estimation from, noisy biophysical recordings. PMID:19424506
Designing and encoding models for synthetic biology. PMID:19364720
Dendritic excitability and neuronal morphology as determinants of synaptic efficacy. PMID:19176614
Low-dimensional, morphologically accurate models of subthreshold membrane potential. PMID:19172386
Brian: a simulator for spiking neural networks in python. PMID:19115011
Roles of axonal sodium channels in precise auditory time coding at nucleus magnocellularis of the chick. PMID:19001045
The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers. PMID:18975149
Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models. PMID:18974796
Dominant ionic mechanisms explored in spiking and bursting using local low-dimensional reductions of a biophysically realistic model neuron. PMID:18594958
Computer modelling of epilepsy. PMID:18594562
A comparative computer simulation of dendritic morphology. PMID:18483611
MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. PMID:17873371
SenseLab: new developments in disseminating neuroscience information. PMID:17510162
neuroConstruct: a tool for modeling networks of neurons in 3D space. PMID:17442244
Capturing the bursting dynamics of a two-cell inhibitory network using a one-dimensional map. PMID:17440801
Parameter estimate of signal transduction pathways. PMID:17118160
Neural Query System: Data-mining from within the NEURON simulator. PMID:16845167
Where is the spike generator of the cochlear nerve? Voltage-gated sodium channels in the mouse cochlea. PMID:16033895
Independent variable time-step integration of individual neurons for network simulations. PMID:15829094 -
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
PubMed citations: 78.
78 articles citing: Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. PMID:35832575
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
EDEN: A High-Performance, General-Purpose, NeuroML-Based Neural Simulator. PMID:35669596
Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks. PMID:35655652
BioSimulators: a central registry of simulation engines and services for recommending specific tools. PMID:35524558
A Phenomenological Mouse Circadian Pacemaker Model. PMID:35485260
Neuron-Glia Interactions and Brain Circuits. PMID:35471536
Conditions for Synaptic Specificity during the Maintenance Phase of Synaptic Plasticity. PMID:35443991
Effects of transcranial alternating current stimulation on spiking activity in computational models of single neocortical neurons. PMID:35093517
Integration of neural architecture within a finite element framework for improved neuromusculoskeletal modeling. PMID:34836986
Resurgent Na+ currents promote ultrafast spiking in projection neurons that drive fine motor control. PMID:34799550
MorphoSONIC: A morphologically structured intramembrane cavitation model reveals fiber-specific neuromodulation by ultrasound. PMID:34585122
The EBRAINS NeuroFeatureExtract: An Online Resource for the Extraction of Neural Activity Features From Electrophysiological Data. PMID:34512300
Modeling NaV1.1/SCN1A sodium channel mutations in a microcircuit with realistic ion concentration dynamics suggests differential GABAergic mechanisms leading to hyperexcitability in epilepsy and hemiplegic migraine. PMID:34314446
Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda. PMID:34282528
Altered A-type potassium channel function impairs dendritic spike initiation and temporoammonic long-term potentiation in Fragile X syndrome. PMID:34083256
Polynomial, piecewise-Linear, Step (PLS): A Simple, Scalable, and Efficient Framework for Modeling Neurons. PMID:34025382
M1-Type, but Not M4-Type, Melanopsin Ganglion Cells Are Physiologically Tuned to the Central Circadian Clock. PMID:34025341
Adherens junction engagement regulates functional patterning of the cardiac pacemaker cell lineage. PMID:33891897
A new reduced-morphology model for CA1 pyramidal cells and its validation and comparison with other models using HippoUnit. PMID:33828151
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. PMID:33513130
Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses. PMID:33494860
Paranoia and belief updating during a crisis. PMID:33469574
Influence of energy deficiency on the subcellular processes of Substantia Nigra Pars Compacta cell for understanding Parkinsonian neurodegeneration. PMID:33462293
Synchronization of Electrically Coupled Resonate-and-Fire Neurons. PMID:33273894
A general model of hippocampal and dorsal striatal learning and decision making. PMID:33229541
Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex. PMID:33170856
A Multi-Scale Computational Model of Excitotoxic Loss of Dopaminergic Cells in Parkinson's Disease. PMID:33101001
Excitation properties of computational models of unmyelinated peripheral axons. PMID:33085556
Gene-set Enrichment with Mathematical Biology (GEMB). PMID:33034635
Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective. PMID:32993675
Tutorial: a computational framework for the design and optimization of peripheral neural interfaces. PMID:32989306
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Periodicity Pitch Perception. PMID:32581672
Zn2+-induced changes in Cav2.3 channel function: An electrophysiological and modeling study. PMID:32559275
Editorial: Reproducibility and Rigour in Computational Neuroscience. PMID:32536859
Paranoia as a deficit in non-social belief updating. PMID:32452769
Modeling the Effect of Temperature on Membrane Response of Light Stimulation in Optogenetically-Targeted Neurons. PMID:32116619
Network Models Predict That Pyramidal Neuron Hyperexcitability and Synapse Loss in the dlPFC Lead to Age-Related Spatial Working Memory Impairment in Rhesus Monkeys. PMID:32009920
Cross-Frequency Coupling in Descending Motor Pathways: Theory and Simulation. PMID:31992973
Pathogenic Processes Underlying Alzheimer's Disease: Modeling the Effects of Amyloid Beta on Synaptic Transmission. PMID:31946282
Unifying Long-Term Plasticity Rules for Excitatory Synapses by Modeling Dendrites of Cortical Pyramidal Neurons. PMID:31875541
Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator. PMID:31803040
Quantitative firing pattern phenotyping of hippocampal neuron types. PMID:31784578
Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms. PMID:31767896
Mechanisms of GABAB receptor enhancement of extrasynaptic GABAA receptor currents in cerebellar granule cells. PMID:31723152
BioModels-15 years of sharing computational models in life science. PMID:31701150
Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity. PMID:31658260
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Introducing double bouquet cells into a modular cortical associative memory model. PMID:31502234
Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity. PMID:31425510
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. PMID:31201122
NetPyNE, a tool for data-driven multiscale modeling of brain circuits. PMID:31025934
A computational model of large conductance voltage and calcium activated potassium channels: implications for calcium dynamics and electrophysiology in detrusor smooth muscle cells. PMID:31025235
Interactions between Membrane Resistance, GABA-A Receptor Properties, Bicarbonate Dynamics and Cl--Transport Shape Activity-Dependent Changes of Intracellular Cl- Concentration. PMID:30897846
A Computational Model of Loss of Dopaminergic Cells in Parkinson's Disease Due to Glutamate-Induced Excitotoxicity. PMID:30858799
Outgrowing seizures in Childhood Absence Epilepsy: time delays and bistability. PMID:30737596
Visualization of currents in neural models with similar behavior and different conductance densities. PMID:30702427
A mathematical model of synaptotagmin 7 revealing functional importance of short-term synaptic plasticity. PMID:30632502
Two Distinct Sets of Ca2+ and K+ Channels Are Activated at Different Membrane Potentials by the Climbing Fiber Synaptic Potential in Purkinje Neuron Dendrites. PMID:30630881
Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0. PMID:30618697
A Metric for Evaluating Neural Input Representation in Supervised Learning Networks. PMID:30618549
Large and fast human pyramidal neurons associate with intelligence. PMID:30561325
Muscle Thickness and Curvature Influence Atrial Conduction Velocities. PMID:30420809
Automated Metadata Suggestion During Repository Submission. PMID:30382537
Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. PMID:30042670
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. PMID:29713272
DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. PMID:29599715
Systematic generation of biophysically detailed models for diverse cortical neuron types. PMID:29459718
A biophysical modelling platform of the cochlear nucleus and other auditory circuits: From channels to networks. PMID:29331233
T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells. PMID:29165247
Computational modeling of spinal circuits controlling limb coordination and gaits in quadrupeds. PMID:29165245
Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. PMID:28970502
A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms. PMID:28863150
Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow. PMID:28770487
Eupnea, tachypnea, and autoresuscitation in a closed-loop respiratory control model. PMID:28724778
Win-win data sharing in neuroscience. PMID:28139675 -
ModelDB: making models publicly accessible to support computational neuroscience
PubMed citations: 51.
51 articles citing: ModelDB: making models publicly accessible to support computational neuroscience
Phase coding of spatial representations in the human entorhinal cortex. PMID:35507662
Acquisition of temporal order requires an intact CA3 commissural/associational (C/A) feedback system in mice. PMID:31286068
Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail. PMID:30377880
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
A biophysical modelling platform of the cochlear nucleus and other auditory circuits: From channels to networks. PMID:29331233
The Endogenous Stress Hormone CRH Modulates Excitatory Transmission and Network Physiology in Hippocampus. PMID:28460009
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. PMID:27760819
A rare schizophrenia risk variant of CACNA1I disrupts CaV3.3 channel activity. PMID:27756899
Automating NEURON Simulation Deployment in Cloud Resources. PMID:27655341
Is realistic neuronal modeling realistic? PMID:27535372
Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim. PMID:27445781
A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. PMID:27148027
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
ModelView for ModelDB: Online Presentation of Model Structure. PMID:25896640
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Effects of low frequency electric fields on synaptic integration in hippocampal CA1 pyramidal neurons: implications for power line emissions. PMID:25346660
Linking macroscopic with microscopic neuroanatomy using synthetic neuronal populations. PMID:25340814
1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time. PMID:25120463
ModelDB in computational neuroscience education - a research tool as interactive educational media. PMID:25089156
NeuroElectro: a window to the world's neuron electrophysiology data. PMID:24808858
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB. PMID:24234915
Frequency dependence of signal power and spatial reach of the local field potential. PMID:23874180
Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. PMID:23678009
Genotype-phenotype correlations in neonatal epilepsies caused by mutations in the voltage sensor of K(v)7.2 potassium channel subunits. PMID:23440208
Control over stress, but not stress per se increases prefrontal cortical pyramidal neuron excitability. PMID:22973008
Computational modeling of epilepsy for an experimental neurologist. PMID:22617489
Differential effects of Kv7 (M-) channels on synaptic integration in distinct subcellular compartments of rat hippocampal pyramidal neurons. PMID:22041186
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models. PMID:21559300
Inverse current source density method in two dimensions: inferring neural activation from multielectrode recordings. PMID:21409556
Postsynaptic signal transduction models for long-term potentiation and depression. PMID:21188161
Automated reconstruction of neuronal morphology: an overview. PMID:21118703
Neuroinformatics: from bioinformatics to databasing the brain. PMID:19812780
Concierge: personal database software for managing digital research resources. PMID:18974800
Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. PMID:18855673
Why are computational neuroscience and systems biology so separate? PMID:18516226
Functional significance of axonal Kv7 channels in hippocampal pyramidal neurons. PMID:18515424
A comparative computer simulation of dendritic morphology. PMID:18483611
Model structure analysis in NEURON : toward interoperability among neural simulators. PMID:18368362
Interoperability of neuroscience modeling software: current status and future directions. PMID:17873374
NeuroMorpho.Org: a central resource for neuronal morphologies. PMID:17728438
SenseLab: new developments in disseminating neuroscience information. PMID:17510162
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. PMID:16381960
Signal propagation in oblique dendrites of CA1 pyramidal cells. PMID:16293591
A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks. PMID:16284416
Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation. PMID:15365194
ModelDB: A Database to Support Computational Neuroscience. PMID:15218350
ModelDB, neuroinformatics, and computational neuroscience. PMID:15055400
Axiope: data sharing using distributed catalogs. PMID:15046249
Text mining neuroscience journal articles to populate neuroscience databases. PMID:15046245 -
ModelDB: an environment for running and storing computational models and their results applied to neuroscience
PubMed citations: 15.
15 articles citing: ModelDB: an environment for running and storing computational models and their results applied to neuroscience
Tutorial: a computational framework for the design and optimization of peripheral neural interfaces. PMID:32989306
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. PMID:29713272
Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. PMID:27760819
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. PMID:27629590
Is realistic neuronal modeling realistic? PMID:27535372
Towards a real-time interface between a biomimetic model of sensorimotor cortex and a robotic arm. PMID:26709323
Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. PMID:25734493
Reinforcement learning of two-joint virtual arm reaching in a computer model of sensorimotor cortex. PMID:24047323
Neuroinformatics: from bioinformatics to databasing the brain. PMID:19812780
SenseLab: new developments in disseminating neuroscience information. PMID:17510162
ModelDB: making models publicly accessible to support computational neuroscience. PMID:15055399
Integration of multidisciplinary sensory data: a pilot model of the human brain project approach. PMID:11141511
Organization of heterogeneous scientific data using the EAV/CR representation. PMID:10579606
Neuronal database integration: the Senselab EAV data model. PMID:10566329
B-SPID: an object-relational database architecture to store, retrieve, and manipulate neuroimaging data. PMID:9950070
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behavior
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ion channel activity
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
neuron
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
software
metasource: Fairsharing.org
version: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
cns models
metasource: re3data.org
version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
brain
metasource: re3data.org
version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
epilepsy
metasource: re3data.org
version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
neurobiology
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version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
neuroinformatics
metasource: re3data.org
version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
synapses
metasource: re3data.org
version: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
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behavior
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ion channel activity
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
neuron
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
software
metasource: Fairsharing.orgversion: FAIRsharing.org: ModelDB; ModelDB; DOI: https://doi.org/10.25504/FAIRsharing.5rb3fk; Last edited: March 9, 2021, 4:06 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
cns models
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
brain
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
epilepsy
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
neurobiology
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
neuroinformatics
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
synapses
metasource: re3data.orgversion: re3data.org: ModelDB; editing status 2022-04-01; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3P61F last accessed: 2022-11-04
behavior ion channel activity mathematical model modeling and simulation network model neuron software cns models brain epilepsy neurobiology neuroinformatics synapses
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