Layer 5 Pyramidal Neuron (Shai et al., 2015)

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Accession:180373
This work contains a NEURON model for a layer 5 pyramidal neuron (based on Hay et al., 2011) with distributed groups of synapses across the basal and tuft dendrites. The results of that simulation are used to fit a phenomenological model, which is also included in this file.
Reference:
1 . Shai AS, Anastassiou CA, Larkum ME, Koch C (2015) Physiology of layer 5 pyramidal neurons in mouse primary visual cortex: coincidence detection through bursting. PLoS Comput Biol 11:e1004090 [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):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Dendritic Action Potentials; Active Dendrites;
Implementer(s):
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Glutamate;
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ShaiEtAl2015
simulationcode
Ca_HVA.mod *
Ca_LVAst.mod *
CaDynamics_E2.mod *
epsp.mod *
glutamate.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
SK_E2.mod *
SKv3_1.mod *
AccessoryFunctions.hoc
DefineSections.hoc
distSynsCluster.hoc
distSynsCluster2.hoc
distSynsUniform.hoc
distSynsUniform2.hoc
distSynsUniformAlpha.hoc
Fig3A.hoc
neuron203.os
O_vd_C.dat
O_vs_C.dat
Run.hoc
varycolor.m
                            
function ColorSet=varycolor(NumberOfPlots)
% VARYCOLOR Produces colors with maximum variation on plots with multiple
% lines.
%
%     VARYCOLOR(X) returns a matrix of dimension X by 3.  The matrix may be
%     used in conjunction with the plot command option 'color' to vary the
%     color of lines.  
%
%     Yellow and White colors were not used because of their poor
%     translation to presentations.
% 
%     Example Usage:
%         NumberOfPlots=50;
%
%         ColorSet=varycolor(NumberOfPlots);
% 
%         figure
%         hold on;
% 
%         for m=1:NumberOfPlots
%             plot(ones(20,1)*m,'Color',ColorSet(m,:))
%         end

%Created by Daniel Helmick 8/12/2008

error(nargchk(1,1,nargin))%correct number of input arguements??
error(nargoutchk(0, 1, nargout))%correct number of output arguements??

%Take care of the anomolies
if NumberOfPlots<1
    ColorSet=[];
elseif NumberOfPlots==1
    ColorSet=[0 1 0];
elseif NumberOfPlots==2
    ColorSet=[0 1 0; 0 1 1];
elseif NumberOfPlots==3
    ColorSet=[0 1 0; 0 1 1; 0 0 1];
elseif NumberOfPlots==4
    ColorSet=[0 1 0; 0 1 1; 0 0 1; 1 0 1];
elseif NumberOfPlots==5
    ColorSet=[0 1 0; 0 1 1; 0 0 1; 1 0 1; 1 0 0];
elseif NumberOfPlots==6
    ColorSet=[0 1 0; 0 1 1; 0 0 1; 1 0 1; 1 0 0; 0 0 0];

else %default and where this function has an actual advantage

    %we have 5 segments to distribute the plots
    EachSec=floor(NumberOfPlots/5); 
    
    %how many extra lines are there? 
    ExtraPlots=mod(NumberOfPlots,5); 
    
    %initialize our vector
    ColorSet=zeros(NumberOfPlots,3);
    
    %This is to deal with the extra plots that don't fit nicely into the
    %segments
    Adjust=zeros(1,5);
    for m=1:ExtraPlots
        Adjust(m)=1;
    end
    
    SecOne   =EachSec+Adjust(1);
    SecTwo   =EachSec+Adjust(2);
    SecThree =EachSec+Adjust(3);
    SecFour  =EachSec+Adjust(4);
    SecFive  =EachSec;

    for m=1:SecOne
        ColorSet(m,:)=[0 1 (m-1)/(SecOne-1)];
    end

    for m=1:SecTwo
        ColorSet(m+SecOne,:)=[0 (SecTwo-m)/(SecTwo) 1];
    end
    
    for m=1:SecThree
        ColorSet(m+SecOne+SecTwo,:)=[(m)/(SecThree) 0 1];
    end
    
    for m=1:SecFour
        ColorSet(m+SecOne+SecTwo+SecThree,:)=[1 0 (SecFour-m)/(SecFour)];
    end

    for m=1:SecFive
        ColorSet(m+SecOne+SecTwo+SecThree+SecFour,:)=[(SecFive-m)/(SecFive) 0 0];
    end
    
end

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