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, K├Âtter 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;
//Display of Vm in all compartments of layer 5 pyramidal cell morphology
create xform /cellform [0%, 0%, 40%, 80%]
create xdraw /cellform/draw [0,0,100%,100%]
setfield /cellform/draw xmin -2.0e-4 xmax 5.0e-4 ymin -2.0e-4 ymax 12.0e-4 zmin -20e-5 zmax 50e-6 bg white
xshow /cellform
create xcell /cellform/draw/cell
setfield /cellform/draw/cell colmin -0.1 colmax 0.05 path /L5P/##[TYPE=compartment] field Vm
useclock /cellform/draw/cell 1
xcolorscale hot


//Graph of somatic Vm
create xform /data1 [0%, 0%, 33%, 33%]
create xgraph /data1/DS1_141099

setfield /data1/DS1_141099 XUnits sec YUnits Volts
setfield /data1/DS1_141099 xmax {tmax} ymin -0.11 ymax 0.04 bg white
useclock /data1/DS1_141099 1	

addmsg /L5P/soma /data1/DS1_141099 PLOT Vm *Soma_Vm *red

xshow /data1


//Graph of somatic conductances
create xform /data2 [0%, 0%, 100%, 100%]
create xgraph /data2/Conductance

setfield /data2/Conductance XUnits sec YUnits S
setfield /data2/Conductance xmax {tmax} ymin 0 ymax 1e-8 bg white
	
addmsg /L5P/soma/NaF /data2/Conductance PLOT Gk *NaF *red
addmsg /L5P/soma/NaP /data2/Conductance PLOT Gk *NaP *orange
addmsg /L5P/soma/KDr /data2/Conductance PLOT Gk *KDr *blue
addmsg /L5P/soma/KA /data2/Conductance PLOT Gk *KA *black
addmsg /L5P/soma/KC /data2/Conductance PLOT Gk *KC *purple
addmsg /L5P/soma/KAHP /data2/Conductance PLOT Gk *KAHP *green
addmsg /L5P/soma/K2 /data2/Conductance PLOT Gk *K2 *brown
addmsg /L5P/soma/KM /data2/Conductance PLOT Gk *KM *grey
addmsg /L5P/soma/CaT /data2/Conductance PLOT Gk *CaT *yellow
addmsg /L5P/soma/CaL /data2/Conductance PLOT Gk *CaL *pink
addmsg /L5P/soma/H /data2/Conductance PLOT Gk *H *cyan


xshow /data2


//Graph of somatic currents
create xform /data3 [0%, 0%, 100%, 100%]
create xgraph /data3/Currents

setfield /data3/Currents XUnits sec YUnits A
setfield /data3/Currents xmax {tmax} ymin -5e-10 ymax 5e-10 bg white

addmsg /L5P/soma/NaF /data3/Currents PLOT Ik *NaF *red
addmsg /L5P/soma/NaP /data3/Currents PLOT Ik *NaP *orange
addmsg /L5P/soma/KDr /data3/Currents PLOT Ik *KDr *blue
addmsg /L5P/soma/KA /data3/Currents PLOT Ik *KA *black
addmsg /L5P/soma/KC /data3/Currents PLOT Ik *KC *purple
addmsg /L5P/soma/KAHP /data3/Currents PLOT Ik *KAHP *green
addmsg /L5P/soma/K2 /data3/Currents PLOT Ik *K2 *brown
addmsg /L5P/soma/KM /data3/Currents PLOT Ik *KM *grey
addmsg /L5P/soma/CaT /data3/Currents PLOT Ik *CaT *yellow
addmsg /L5P/soma/CaL /data3/Currents PLOT Ik *CaL *pink
addmsg /L5P/soma/H /data3/Currents PLOT Ik *H *cyan
	
xshow /data3





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