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

 Download zip file   Auto-launch 
Help downloading and running models
These are the NEURON files for 10 different models of a reduced L5 pyramidal neuron. The parameters were obtained by automatically fitting the models to experimental data using a multi objective evolutionary search strategy. Details on the algorithm can be found at <a href="http://www.g-node.org/emoo">www.g-node.org/emoo</a> and in Bahl et al. (2012).
1 . Bahl A, Stemmler MB, Herz AV, Roth A (2012) Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. J Neurosci Methods 210:22-34 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex layer 5-6 pyramidal cell;
Channel(s): I Na,p; I Na,t; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions:
Simulation Environment: NEURON; Python;
Model Concept(s): Action Potential Initiation; Parameter Fitting; Simplified Models; Active Dendrites; Detailed Neuronal Models; Action Potentials; Methods; Calcium dynamics;
Implementer(s): Bahl, Armin [bahl at neuro.mpg.de];
Search NeuronDB for information about:  Neocortex layer 5-6 pyramidal cell; I Na,p; I Na,t; I K; I M; I h; I K,Ca; I Calcium; I A, slow;

Bahl A, Stemmler MB, Herz AV, Roth A (2012) Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. J Neurosci Methods 210:22-34[PubMed]

References and models cited by this paper

References and models that cite this paper

Achard P, De Schutter E (2006) Complex parameter landscape for a complex neuron model. PLoS Comput Biol 2:e94 [PubMed]

Bekkers JM, Hausser M (2007) Targeted dendrotomy reveals active and passive contributions of the dendritic tree to synaptic integration and neuronal output. Proc Natl Acad Sci U S A 104:11447-52 [PubMed]

Berger T, Larkum ME, Luscher HR (2001) High I(h) channel density in the distal apical dendrite of layer V pyramidal cells increases bidirectional attenuation of EPSPs. J Neurophysiol 85:855-68 [Journal] [PubMed]

Borst A, Haag J (1996) The intrinsic electrophysiological characteristics of fly lobula plate tangential cells: I. Passive membrane properties. J Comput Neurosci 3:313-36 [Journal] [PubMed]

   [11 reconstructed morphologies on NeuroMorpho.Org]
   Fly lobular plate VS cell (Borst and Haag 1996, et al. 1997, et al. 1999) [Model]

Branco T, Clark BA, Hausser M (2010) Dendritic Discrimination of Temporal Input Sequences in Cortical Neurons. Science 329(5999):1671-1675 [Journal] [PubMed]

   Dendritic Discrimination of Temporal Input Sequences (Branco et al. 2010) [Model]

Bush PC, Sejnowski TJ (1993) Reduced compartmental models of neocortical pyramidal cells. J Neurosci Methods 46:159-66 [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

Colbert CM, Pan E (2002) Ion channel properties underlying axonal action potential initiation in pyramidal neurons. Nat Neurosci 5:533-8 [PubMed]

Deb K (2001) Multi-objective optimization using evolutionary algorithms xix:1-497

Deb K, Agrawal RB (1995) Simulated binary crossover for continuous search space Complex Syst 9:115-48

Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II Nsga-ii Ieee Transactions On Evolutionary Computation 6:182-197

Destexhe A (2001) Simplified models of neocortical pyramidal cells preserving somatodendritic voltage attenuation Neurocomputing 38-40:167-173

Druckmann S, Banitt Y, Gidon A, Schurmann F, Markram H, Segev I (2007) A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data. Front Neurosci 1:7-18 [PubMed]

Druckmann S, Berger TK, Hill S, Schurmann F, Markram H, Segev I (2008) Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data. Biol Cybern 99:371-9 [PubMed]

Druckmann S, Berger TK, Schurmann F, Hill S, Markram H, Segev I (2011) Effective Stimuli for Constructing Reliable Neuron Models PLoS Comput Biol 7(8):e1002133 [Journal]

Eckmann J, Ruelle D (1985) Ergodic theory of chaos and strange attractors Rev Mod Phys 57:617-656

Fox SE (1985) Location of membrane conductance changes by analysis of the input impedance of neurons. I. Theory. J Neurophysiol 54:1578-93

Goldman MS, Golowasch J, Marder E, Abbott LF (2001) Global structure, robustness, and modulation of neuronal models. J Neurosci 21:5229-38 [Journal] [PubMed]

   Global structure, robustness, and modulation of neuronal models (Goldman et al. 2001) [Model]

Golowasch J, Goldman MS, Abbott LF, Marder E (2002) Failure of averaging in the construction of a conductance-based neuron model. J Neurophysiol 87:1129-31 [Journal] [PubMed]

Hay E, Hill S, Schurmann F, Markram H, Segev I (2011) Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS Comput Biol 7:e1002107 [Journal] [PubMed]

   [3 reconstructed morphologies on NeuroMorpho.Org]
   L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) [Model]

Herz AV, Gollisch T, Machens CK, Jaeger D (2006) Modeling single-neuron dynamics and computations: a balance of detail and abstraction. Science 314:80-5 [PubMed]

Hille B (2001) Ionic Channels of Excitable Membranes

Hines ML, Davison AP, Muller E (2009) NEURON and Python Frontiers in Neuroinformatics 3:1 [Journal] [PubMed]

   NEURON + Python (Hines et al. 2009) [Model]

Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11 [Journal] [PubMed]

Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [Journal] [PubMed]

   Squid axon (Hodgkin, Huxley 1952) (LabAXON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (NEURON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SNNAP) [Model]
   Squid axon (Hodgkin, Huxley 1952) used in (Chen et al 2010) (R language) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other) [Model]

Kennel MB, Brown R, Abarbanel HD (1992) Determining embedding dimension for phase-space reconstruction using a geometrical construction. Phys Rev A 45:3403-3411 [PubMed]

Keren N, Bar-Yehuda D, Korngreen A (2009) Experimentally guided modelling of dendritic excitability in rat neocortical pyramidal neurones. J Physiol 587:1413-37 [PubMed]

Keren N, Peled N, Korngreen A (2005) Constraining compartmental models using multiple voltage recordings and genetic algorithms. J Neurophysiol 94:3730-42 [Journal] [PubMed]

Kole MH, Hallermann S, Stuart GJ (2006) Single Ih channels in pyramidal neuron dendrites: properties, distribution, and impact on action potential output. J Neurosci 26:1677-87 [Journal] [PubMed]

   Stochastic Ih and Na-channels in pyramidal neuron dendrites (Kole et al 2006) [Model]

Kole MH, Ilschner SU, Kampa BM, Williams SR, Ruben PC, Stuart GJ (2008) Action potential generation requires a high sodium channel density in the axon initial segment. Nat Neurosci 11:178-86 [Journal] [PubMed]

   Na+ channel dependence of AP initiation in cortical pyramidal neuron (Kole et al. 2008) [Model]

Kole MH, Letzkus JJ, Stuart GJ (2007) Axon initial segment Kv1 channels control axonal action potential waveform and synaptic efficacy. Neuron 55:633-47 [PubMed]

Kole MH, Stuart GJ (2008) Is action potential threshold lowest in the axon? Nat Neurosci 11:1253-5 [PubMed]

Korngreen A, Sakmann B (2000) Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients. J Physiol 525 Pt 3:621-39 [PubMed]

   Pyramidal Neuron Deep: K+ kinetics (Korngreen, Sakmann 2000) [Model]

Larkum ME, Senn W, Luscher HR (2004) Top-down dendritic input increases the gain of layer 5 pyramidal neurons. Cereb Cortex 14:1059-70 [PubMed]

Larkum ME, Zhu JJ, Sakmann B (1999) A new cellular mechanism for coupling inputs arriving at different cortical layers. Nature 398:338-41 [PubMed]

Larkum ME, Zhu JJ, Sakmann B (2001) Dendritic mechanisms underlying the coupling of the dendritic with the axonal action potential initiation zone of adult rat layer 5 pyramidal neurons. J Physiol 533:447-66 [PubMed]

LeMasson G, Maex R (2001) Introduction to equation solving and parameter fitting Computational Neuroscience: Realistic Modelling for Experimentalists, De Schutter E, ed. pp.1

Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39 [PubMed]

   Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995) [Model]

Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6 [Journal] [PubMed]

   [2 reconstructed morphologies on NeuroMorpho.Org]
   Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996) [Model]

Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]

   [241 reconstructed morphologies on NeuroMorpho.Org]

Metz AE, Spruston N, Martina M (2007) Dendritic D-type potassium currents inhibit the spike afterdepolarization in rat hippocampal CA1 pyramidal neurons. J Physiol 581:175-87 [PubMed]

Naundorf B, Geisel T, Wolf F (2005) Action potential onset dynamics and the response speed of neuronal populations. J Comput Neurosci 18:297-309 [PubMed]

Nevian T, Larkum ME, Polsky A, Schiller J (2007) Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study. Nat Neurosci 10:206-14 [Journal] [PubMed]

   Dendritic Na+ spike initiation and backpropagation of APs in active dendrites (Nevian et al. 2007) [Model]

Palmer LM, Stuart GJ (2006) Site of action potential initiation in layer 5 pyramidal neurons. J Neurosci 26:1854-63 [PubMed]

Poirazi P, Brannon T, Mel BW (2003a) Arithmetic of subthreshold synaptic summation in a model CA1 pyramidal cell. Neuron 37:977-987 [Journal] [PubMed]

   CA1 pyramidal neuron: as a 2-layer NN and subthreshold synaptic summation (Poirazi et al 2003) [Model]

Popovic MA, Foust AJ, McCormick DA, Zecevic D (2011) The spatio-temporal characteristics of action potential initiation in layer 5 pyramidal neurons: a voltage imaging study. J Physiol 589:4167-87 [PubMed]

Prinz AA, Billimoria CP, Marder E (2003) Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. J Neurophysiol 90:3998-4015 [Journal] [PubMed]

Prinz AA, Bucher D, Marder E (2004) Similar network activity from disparate circuit parameters. Nat Neurosci 7:1345-52 [PubMed]

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

RALL W (1962) Theory of physiological properties of dendrites. Ann N Y Acad Sci 96:1071-92 [PubMed]

Roth A, Bahl A (2009) Divide et impera: optimizing compartmental models of neurons step by step. J Physiol 587:1369-70 [PubMed]

Rush AM, Dib-Hajj SD, Waxman SG (2005) Electrophysiological properties of two axonal sodium channels, Nav1.2 and Nav1.6, expressed in mouse spinal sensory neurones. J Physiol 564:803-15 [PubMed]

Schaefer AT, Larkum ME, Sakmann B, Roth A (2003) Coincidence detection in pyramidal neurons is tuned by their dendritic branching pattern. J Neurophysiol 89:3143-54 [Journal] [PubMed]

   Pyramidal neuron coincidence detection tuned by dendritic branching pattern (Schaefer et al 2003) [Model]

Schiller J, Schiller Y, Stuart G, Sakmann B (1997) Calcium action potentials restricted to distal apical dendrites of rat neocortical pyramidal neurons. J Physiol 505 ( Pt 3):605-16 [PubMed]

Schulz DJ, Goaillard JM, Marder E (2006) Variable channel expression in identified single and electrically coupled neurons in different animals. Nat Neurosci 9:356-62 [PubMed]

Stratford KJ, Mason AJR, Larkman AU, Major G, Jack JJB (1989) The modelling of pyramidal neurones in the visual cortex The Computing Neuron, Durbin R:Miall C:Mitchison G, ed. pp.296

Stuart G, Schiller J, Sakmann B (1997) Action potential initiation and propagation in rat neocortical pyramidal neurons. J Physiol 505 ( Pt 3):617-32 [PubMed]

Stuart G, Spruston N (1998) Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. J Neurosci 18:3501-10 [PubMed]

   [13 reconstructed morphologies on NeuroMorpho.Org]
   Pyramidal Neuron Deep: attenuation in dendrites (Stuart, Spruston 1998) [Model]

Stuart GJ, Sakmann B (1994) Active propagation of somatic action potentials into neocortical pyramidal cell dendrites. Nature 367:69-72 [PubMed]

Takens F (1981) Detecting strange attractors in turbulence in dynamical systems and turbulence Lecture Notes In Mathematics 898:366-381

Taylor AL, Goaillard JM, Marder E (2009) How multiple conductances determine electrophysiological properties in a multicompartment model. J Neurosci 29:5573-86 [PubMed]

Traub RD, Buhl EH, Gloveli T, Whittington MA (2003) Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na(+) Conductance or by Blocking BK Channels. J Neurophysiol 89:909-21 [Journal] [PubMed]

   Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003) [Model]

Traub RD, Contreras D, Cunningham MO, Murray H, Lebeau FE, Roopun A, Bibbig A, et al (2005) A single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles and epileptogenic bursts J Neurophysiol 93(4):2194-232 [Journal] [PubMed]

   A single column thalamocortical network model (Traub et al 2005) [Model]

Wheeler BC, Smith SR (1988) High-resolution alignment of action potential waveforms using cubic spline interpolation. J Biomed Eng 10:47-53 [PubMed]

Winograd M, Destexhe A, Sanchez-Vives MV (2008) Hyperpolarization-activated graded persistent activity in the prefrontal cortex. Proc Natl Acad Sci U S A 105:7298-303 [Journal] [PubMed]

   Hodgkin-Huxley model of persistent activity in prefrontal cortex neurons (Winograd et al. 2008) [Model]
   Hodgkin-Huxley model of persistent activity in PFC neurons (Winograd et al. 2008) (NEURON python) [Model]

Yu Y, Shu Y, McCormick DA (2008) Cortical action potential backpropagation explains spike threshold variability and rapid-onset kinetics. J Neurosci 28:7260-72 [Journal] [PubMed]

   AP back-prop. explains threshold variability and rapid rise (McCormick et al. 2007, Yu et al. 2008) [Model]

Zhu JJ (2000) Maturation of layer 5 neocortical pyramidal neurons: amplifying salient layer 1 and layer 4 inputs by Ca2+ action potentials in adult rat tuft dendrites. J Physiol 526 Pt 3:571-87 [PubMed]

Friedrich P, Vella M, Gulyas AI, Freund TF, Kali S (2014) A flexible, interactive software tool for fitting the parameters of neuronal models. Front Neuroinform 8:63 [Journal] [PubMed]

   Software (called Optimizer) for fitting neuronal models (Friedrich et al. 2014) [Model]

Hay E, Schurmann F, Markram H, Segev I (2013) Preserving Axo-somatic Spiking Features Despite Diverse Dendritic Morphology. J Neurophysiol 109(12):2972-81 [Journal] [PubMed]

   [4 reconstructed morphologies on NeuroMorpho.Org]
   Preserving axosomatic spiking features despite diverse dendritic morphology (Hay et al., 2013) [Model]

Maki-Marttunen T, Halnes G, Devor A, Witoelar A, Bettella F, Djurovic S, Wang Y, Einevoll GT, (2016) Functional Effects of Schizophrenia-Linked Genetic Variants on Intrinsic Single-Neuron Excitability: A Modeling Study. Biol Psychiatry Cogn Neurosci Neuroimaging 1:49-59 [Journal] [PubMed]

   Schiz.-linked gene effects on intrinsic single-neuron excitability (Maki-Marttunen et al. 2016) [Model]

Marasco A, Limongiello A, Migliore M (2013) Using Strahler`s analysis to reduce up to 200-fold the run time of realistic neuron model Sci. Rep. 3:2934 [Journal] [PubMed]

   Using Strahler`s analysis to reduce realistic models (Marasco et al, 2013) [Model]

Zylbertal A, Kahan A, Ben-Shaul Y, Yarom Y, Wagner S (2015) Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells PLOS Biology 13(12):e1002319 [Journal]

   AOB mitral cell: persistent activity without feedback (Zylbertal et al., 2015) [Model]

(71 refs)