Pyramidal Neuron Deep: Constrained by experiment (Dyhrfjeld-Johnsen et al. 2005)

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Accession:93349
"... As a practical demonstration of the use of CoCoDat we constructed a detailed computer model of an intrinsically bursting (IB) layer V pyramidal neuron from the rat barrel cortex supplementing experimental data (Schubert et al., 2001) with information extracted from the database. The pyramidal neuron morphology (Fig. 10B) was reconstructed from histological sections of a biocytin-stained IB neuron using the NeuroLucida software package..."
Reference:
1 . Dyhrfjeld-Johnsen J, Maier J, Schubert D, Staiger J, Luhmann HJ, Stephan KE, Kötter R (2005) CoCoDat: a database system for organizing and selecting quantitative data on single neurons and neuronal microcircuitry. J Neurosci Methods 141:291-308 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): 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;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Bursting;
Implementer(s): Dyhrfjeld-Johnsen, Jonas [jdyhrfje at uci.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; 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; 
This collection of scripts are used to simulate IV curves from a layer
5 pyramidal cell from rat somatosensory (barrel) cortex as shown in
Fig.11 of


Dyhrfjeld-Johnsen J,Maier J,Schubert D,Staiger J,Luhmann HJ,Stephan
KE, Kotter R.: CoCoDat: a database system for organizing and selecting
quantitative data on single neurons and neuronal microcircuitry. J
Neurosci Methods. 2005 Feb 15;141(2):291-308.


The scripts involved are:

* L5P_mainloop.g - The main simulation script that executes the setup
of the model and runs through the series of current injections.

*L5P_const.g - Constants and values used in the simulation.

*DS1_141099_rot2_sc_defmesh.p - The reconstructed neuron morphology.

*L5P_chans.g - Tabchannel definitions of ion-channels used in the
simulation

*L5P_comps.g - Protope compartments used for setting up the model.

*DiffRm.g & Hgradient.g - Functions to set up differentially
distributed values for Rm and H-current density.

*L5P_input.g & ExpInjCur.g - Scripts to set up (and provide amplitudes
for) current injection stimulation.

*L5P_graph.g - Creates direct graphical output of membrane potential
for entire morphology, somatic Vm, somatic conductances and somatic
currents. Graphic output can be turned off by commenting out line 40
in the main simulation script.

L5P_ascout.g - Script to write out somatic voltage traces to ASCII
format. ASCII output can be turned off by commenting out line 41 in
the main simulation script.

*DS991014IVPotential.asc - The experimentally recorded IV curves for
the modeled cell.

*plotVmIBloop.m - MATLAB script to plot the simulated and
experimentally recorded IV curves in the same graph for comparison.

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