Parameter estimation for Hodgkin-Huxley based models of cortical neurons (Lepora et al. 2011)

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Accession:136808
Simulation and fitting of two-compartment (active soma, passive dendrite) for different classes of cortical neurons. The fitting technique indirectly matches neuronal currents derived from somatic membrane potential data rather than fitting the voltage traces directly. The method uses an analytic solution for the somatic ion channel maximal conductances given approximate models of the channel kinetics, membrane dynamics and dendrite. This approach is tested on model-derived data for various cortical neurons.
Reference:
1 . Lepora NF, Overton PG, Gurney K (2012) Efficient fitting of conductance-based model neurons from somatic current clamp. J Comput Neurosci 32:1-24 [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; Neocortex L2/3 pyramidal GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,t; I L high threshold; I T low threshold; I K; I M;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Parameter Fitting; Simplified Models; Parameter sensitivity;
Implementer(s): Lepora, Nathan [n.lepora at shef.ac.uk];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; I Na,t; I L high threshold; I T low threshold; I K; I M;
function simDend_1act1pas(id, t,Vs, CM,RM,RA,Em,len,dia, dir_sim,dir_model)

% ensure names of appropriate format for genesis
wdir = cd; cd ~; hdir = cd; cd(wdir); 
if all(~strcmp(dir_sim(1),{'/','~'})); dir_sim = [wdir,'/',dir_sim]; end
if strcmp(dir_sim(1),'~'); dir_sim = [hdir,dir_sim(2:end)]; end
if all(~strcmp(dir_model(1),{'/','~'})); dir_model = [wdir,'/',dir_model]; end
if strcmp(dir_model(1),'~'); dir_model = [hdir,dir_model(2:end)]; end

% save voltage
if ~isdir(dir_sim); mkdir(dir_sim); end; cd(dir_sim);
if ~isdir([dir_sim,'/voltage']); mkdir([dir_sim,'/voltage']); end
for j = 1:size(Vs,2)
    file_voltage{j} = [dir_sim,'/voltage/voltage',num2str(j),'.dat ']; 
    tV = [t,Vs(:,j)]; save(file_voltage{j}(1:end-1),'tV','-ascii'); 
end

%% write passive parameters to genesis file

fid = fopen('runSim.g','w');

fprintf(fid,['float CM0=',num2str(CM),'\n']);
fprintf(fid,['float RM0=',num2str(RM),'\n']);
fprintf(fid,['float RA0=',num2str(RA),'\n']);
fprintf(fid,['float Em0=',num2str(Em),'\n']);
fprintf(fid,['float len=',num2str(len(1)),', dia=',num2str(dia(1)),'\n']);
fprintf(fid,['float len1=',num2str(len(2)),', dia1=',num2str(dia(2)),'\n']);

fprintf(fid,'\n');
fprintf(fid,['str files_voltage="',file_voltage{:},'"\n']);
fprintf(fid,['str dir_out="',dir_sim,'"\n']);
fprintf(fid,['include ',dir_model,'/simDend_1act1pas.g\n']);
fclose(fid);

%% run genesis 

[s,d] = system('genesis -nox -notty -batch runSim.g > dump.txt');
cd(wdir)

% report on setting
disp('simDend:');
disp(['dir_sim = "',dir_sim,'"']);
disp(['dir_model = "',dir_model,'"']);
disp(' ')

%% HACK - delete final line of data_Vd (genesis IO problem)

fid = fopen([dir_sim,'/data_Vd.dat'],'r+');
fseek(fid,-1000,'eof'); i = find(fread(fid,1000)==10,1,'last');
fseek(fid,i-1000,'eof'); fprintf(fid,repmat(' ',[1000-i 1]));
fclose(fid);

end

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