Arkhipov A et al. (2018). Visual physiology of the layer 4 cortical circuit in silico. PLoS computational biology. 14 [PubMed]

• Visual physiology of the layer 4 cortical circuit in silico (Arkhipov et al 2018) [Model]

Aumentado-Armstrong T, Metzen MG, Sproule MK, Chacron MJ. (2015). Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli. PLoS computational biology. 11 [PubMed]

• Midbrain torus semicircularis neuron model (Aumentado-Armstrong et al. 2015) [Model]

Ausborn J, Stein W, Wolf H. (2007). Frequency control of motor patterning by negative sensory feedback. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27 [PubMed]

• Interaction of leak and IMI conductance on the STG over broad temperature range (Stadele et al 2015) [Model]

Bahl A, Stemmler MB, Herz AV, Roth A. (2012). Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. Journal of neuroscience methods. 210 [PubMed]

• A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012) [Model]

Beer RD. (2006). Parameter space structure of continuous-time recurrent neural networks. Neural computation. 18 [PubMed]

Ben-Shalom R et al. (2022). NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs Journal of neuroscience methods. 366 [PubMed]

• NeuroGPU example on L5_TTPC1_cADpyr232_1 (Ben-Shalom 2022)(Ramaswamy et al., 2015) [Model]

Calin-Jageman RJ, Katz PS. (2006). A distributed computing tool for generating neural simulation databases. Neural computation. 18 [PubMed]

• Distributed computing tool for NEURON, NEURONPM (screensaver) (Calin-Jageman and Katz 2006) [Model]

Caplan JS, Williams AH, Marder E. (2014). Many parameter sets in a multicompartment model oscillator are robust to temperature perturbations. The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]

• Temperature-Dependent Pyloric Pacemaker Kernel (Caplan JS et al., 2014) [Model]

Carey RM, Sherwood WE, Shipley MT, Borisyuk A, Wachowiak M. (2015). Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb. Journal of neurophysiology. 113 [PubMed]

• Olfactory bulb juxtaglomerular models (Carey et al., 2015) [Model]

Carlu M et al. (2020). A mean-field approach to the dynamics of networks of complex neurons, from nonlinear Integrate-and-Fire to Hodgkin-Huxley models. Journal of neurophysiology. 123 [PubMed]

• Mean field model for Hodgkin Huxley networks of neurons (Carlu et al 2020) [Model]

Ceballos CC, Li S, Roque AC, Tzounopoulos T, Leão RM. (2016). Ih Equalizes Membrane Input Resistance in a Heterogeneous Population of Fusiform Neurons in the Dorsal Cochlear Nucleus. Frontiers in cellular neuroscience. 10 [PubMed]

• DCN fusiform cell (Ceballos et al. 2016) [Model]

Conde-Sousa E, Aguiar P. (2013). A working memory model for serial order that stores information in the intrinsic excitability properties of neurons. Journal of computational neuroscience. 35 [PubMed]

• Storing serial order in intrinsic excitability: a working memory model (Conde-Sousa & Aguiar 2013) [Model]

Daur N, Diehl F, Mader W, Stein W. (2012). The stomatogastric nervous system as a model for studying sensorimotor interactions in real-time closed-loop conditions. Frontiers in computational neuroscience. 6 [PubMed]

• Interaction of leak and IMI conductance on the STG over broad temperature range (Stadele et al 2015) [Model]

Doloc-Mihu A, Calabrese RL. (2011). A database of computational models of a half-center oscillator for analyzing how neuronal parameters influence network activity. Journal of biological physics. 37 [PubMed]

• Half-center oscillator database of leech heart interneuron model (Doloc-Mihu & Calabrese 2011) [Model]

Fernandez FR, Mehaffey WH, Turner RW. (2005). Dendritic Na+ current inactivation can increase cell excitability by delaying a somatic depolarizing afterpotential. Journal of neurophysiology. 94 [PubMed]

• Dendritic Na inactivation drives a decrease in ISI (Fernandez et al 2005) [Model]

Golomb D et al. (2007). Mechanisms of firing patterns in fast-spiking cortical interneurons. PLoS computational biology. 3 [PubMed]

• Fast-spiking cortical interneuron (Golomb et al. 2007) [Model]

Gutierrez GJ, O'Leary T, Marder E. (2013). Multiple mechanisms switch an electrically coupled, synaptically inhibited neuron between competing rhythmic oscillators. Neuron. 77 [PubMed]

• Competing oscillator 5-cell circuit and Parameterscape plotting (Gutierrez et al. 2013) [Model]

Günay C, Doloc-Mihu A, Lamb DG, Calabrese RL. (2019). Synaptic Strengths Dominate Phasing of Motor Circuit: Intrinsic Conductances of Neuron Types Need Not Vary across Animals. eNeuro. 6 [PubMed]

• Synaptic strengths are critical in creating the proper output phasing in a CPG (Gunay et al 2019) [Model]

Günay C, Prinz AA. (2010). Model calcium sensors for network homeostasis: sensor and readout parameter analysis from a database of model neuronal networks. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30 [PubMed]

• Lobster STG pyloric network model with calcium sensor (Gunay & Prinz 2010) (Prinz et al. 2004) [Model]

Hemond P et al. (2008). Distinct classes of pyramidal cells exhibit mutually exclusive firing patterns in hippocampal area CA3b. Hippocampus. 18 [PubMed]

• CA3 pyramidal neuron: firing properties (Hemond et al. 2008) [Model]

Hendrickson EB, Edgerton JR, Jaeger D. (2011). The capabilities and limitations of conductance-based compartmental neuron models with reduced branched or unbranched morphologies and active dendrites. Journal of computational neuroscience. 30 [PubMed]

• Comparison of full and reduced globus pallidus models (Hendrickson 2010) [Model]

Huang C, Zeldenrust F, Celikel T. (2022). Cortical Representation of Touch in Silico Neuroinformatics. 20 [PubMed]

• Realistic barrel cortical column - Matlab (Huang et al., 2022) [Model]
• Realistic barrel cortical column - NetPyNE (Huang et al., 2022) [Model]

Jolivet R et al. (2008). A benchmark test for a quantitative assessment of simple neuron models. Journal of neuroscience methods. 169 [PubMed]

• Spike Response Model simulator (Jolivet et al. 2004, 2006, 2008) [Model]

Jȩdrzejewski-Szmek Z, Abrahao KP, Jȩdrzejewska-Szmek J, Lovinger DM, Blackwell KT. (2018). Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Frontiers in neuroinformatics. 12 [PubMed]

• Parameter optimization using CMA-ES (Jedrzejewski-Szmek et al 2018) [Model]

Kretzberg J, Kretschmer F, Marin-Burgin A. (2007). Effects of multiple spike-initiation zones in touch sensory cells of the leech , Volume 70, Issues 10-12, June 2007, Pages 1645-1651 Neurocomputing. 70

Lamb DG, Calabrese RL. (2013). Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PloS one. 8 [PubMed]

• Leech Heart (HE) Motor Neuron conductances contributions to NN activity (Lamb & Calabrese 2013) [Model]

Liu RY et al. (2013). Deficit in long-term synaptic plasticity is rescued by a computationally predicted stimulus protocol. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]

• Rescue of plasticity by a computationally predicted protocol (Liu et al. 2013) [Model]

Marcelin B et al. (2009). h channel-dependent deficit of theta oscillation resonance and phase shift in temporal lobe epilepsy. Neurobiology of disease. 33 [PubMed]

• CA1 pyramidal neuron: h channel-dependent deficit of theta oscill. resonance (Marcelin et al. 2008) [Model]

McKinnon ML et al. (2019). Dramatically Amplified Thoracic Sympathetic Postganglionic Excitability and Integrative Capacity Revealed with Whole-Cell Patch-Clamp Recordings. eNeuro. 6 [PubMed]

• Conductance-based model of rodent thoracic sympathetic postganglionic neuron (McKinnon et al 2019) [Model]

Medlock L et al. (2022). Multiscale computer model of the spinal dorsal horn reveals changes in network processing associated with chronic pain The Journal of neuroscience : the official journal of the Society for Neuroscience. 42 [PubMed]

• Spinal Dorsal Horn Network Model (Medlock et al 2022) [Model]

Mukunda CL, Narayanan R. (2017). Degeneracy in the regulation of short-term plasticity and synaptic filtering by presynaptic mechanisms. The Journal of physiology. 595 [PubMed]

• Conductance based model for short term plasticity at CA3-CA1 synapses (Mukunda & Narayanan 2017) [Model]

Neymotin SA et al. (2017). Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. Journal of neurophysiology. 117 [PubMed]

• Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017) [Model]

Nowotny T, Levi R, Selverston AI. (2008). Probing the dynamics of identified neurons with a data-driven modeling approach. PloS one. 3 [PubMed]

• Data-driven, HH-type model of the lateral pyloric (LP) cell in the STG (Nowotny et al. 2008) [Model]

Nowotny T, Szücs A, Levi R, Selverston AI. (2007). Models wagging the dog: are circuits constructed with disparate parameters? Neural computation. 19 [PubMed]

Olypher AV, Calabrese RL. (2007). Using constraints on neuronal activity to reveal compensatory changes in neuronal parameters. Journal of neurophysiology. 98 [PubMed]

• Activity constraints on stable neuronal or network parameters (Olypher and Calabrese 2007) [Model]

Otopalik AG et al. (2017). Sloppy morphological tuning in identified neurons of the crustacean stomatogastric ganglion. eLife. 6 [PubMed]

• Sloppy morphological tuning in identified neurons of the crustacean STG (Otopalik et al 2017) [Model]

Podlaski WF et al. (2017). Mapping the function of neuronal ion channels in model and experiment. eLife. 6 [PubMed]

Ratté S, Zhu Y, Lee KY, Prescott SA. (2014). Criticality and degeneracy in injury-induced changes in primary afferent excitability and the implications for neuropathic pain. eLife. 3 [PubMed]

• Criticality,degeneracy in injury-induced changes in primary afferent excitability (Ratte et al 2014) [Model]

Rich S, Moradi Chameh H, Sekulic V, Valiante TA, Skinner FK. (2021). Modeling Reveals Human-Rodent Differences in H-Current Kinetics Influencing Resonance in Cortical Layer 5 Neurons. Cerebral cortex (New York, N.Y. : 1991). 31 [PubMed]

• Human Cortical L5 Pyramidal Cell (Rich et al. 2021) [Model]

Rumbell T, Kozloski J. (2019). Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons PLOS Computational Biology. 15

• Control of oscillations and spontaneous firing in dopamine neurons (Rumbell & Kozloski 2019) [Model]

Scheler G. (2013). Learning intrinsic excitability in medium spiny neurons F1000Research. 2 [PubMed]

• Learning intrinsic excitability in Medium Spiny Neurons (Scheler 2014) [Model]

Schwarzacher SW, Cuntz H, Jedlicka P, Beining M, Mongiat LA. (2017). T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife.

• GC model (Beining et al 2017) [Model]
• Mature and young adult-born dentate granule cell models (T2N interface) (Beining et al. 2017) [Model]

Shapiro NP, Lee RH. (2007). Synaptic amplification versus bistability in motoneuron dendritic processing: a top-down modeling approach. Journal of neurophysiology. 97 [PubMed]

Sharples SA et al. (2021). Mechanisms of Episodic Rhythmicity Contributions of h-and Na+/K+ pump currents to the generation of episodic and continuous rhythmic activities Frontiers in cellular neuroscience. 15 [PubMed]

• Mouse Episodic and Continuous Locomotion CPG (Sharples et al, 2022) [Model]

Sousa M, Szucs P, Lima D, Aguiar P. (2014). The pronociceptive dorsal reticular nucleus contains mostly tonic neurons and shows a high prevalence of spontaneous activity in block preparation. Journal of neurophysiology. 111 [PubMed]

• DRt neuron model (Sousa et al., 2014) [Model]

Stein W, Straub O, Ausborn J, Mader W, Wolf H. (2008). Motor pattern selection by combinatorial code of interneuronal pathways. Journal of computational neuroscience. 25 [PubMed]

• A model of the femur-tibia control system in stick insects (Stein et al. 2008) [Model]
• Interaction of leak and IMI conductance on the STG over broad temperature range (Stadele et al 2015) [Model]

Städele C, Heigele S, Stein W. (2015). Neuromodulation to the Rescue: Compensation of Temperature-Induced Breakdown of Rhythmic Motor Patterns via Extrinsic Neuromodulatory Input. PLoS biology. 13 [PubMed]

• Interaction of leak and IMI conductance on the STG over broad temperature range (Stadele et al 2015) [Model]

Tobin AE, Calabrese RL. (2006). Endogenous and half-center bursting in morphologically inspired models of leech heart interneurons. Journal of neurophysiology. 96 [PubMed]

Tobin AE, Van Hooser SD, Calabrese RL. (2006). Creation and reduction of a morphologically detailed model of a leech heart interneuron. Journal of neurophysiology. 96 [PubMed]

Wang YC et al. (2022). Multimodal parameter spaces of a complex multi-channel neuron model Frontiers in systems neuroscience. 16 [PubMed]

• Parallel Tempering MCMC on Liu et al 1998 (Wang et al 2022) [Model]

Weaver CM, Wearne SL. (2006). The role of action potential shape and parameter constraints in optimization of compartment models Neurocomputing. 69

• AP shape and parameter constraints in optimization of compartment models (Weaver and Wearne 2006) [Model]

Webster-Wood VA, Gill JP, Thomas PJ, Chiel HJ. (2020). Control for multifunctionality: bioinspired control based on feeding in Aplysia californica. Biological cybernetics. 114 [PubMed]

• Multifunctional control of feeding in Aplysia (Webster-Wood et al. 2020) [Model]

Yang J, Shakil H, Ratté S, Prescott SA. (2022). Minimal requirements for a neuron to co-regulate many properties and the implications for ion channel correlations and robustness eLife. 11 [PubMed]

• A modified Morris-Lecar model with gM and gAHP (Yang et al., 2022) [Model]

Zang Y, Marder E. (2023). Neuronal morphology enhances robustness to perturbations of channel densities Proceedings of the National Academy of Sciences of the United States of America. 120 [PubMed]

• LP neuron model database (Zang and Marder 2023) [Model]