Gap junction coupled network of striatal fast spiking interneurons (Hjorth et al. 2009)

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Accession:118389
Gap junctions between striatal FS neurons has very weak ability to synchronise spiking. Input uncorrelated between neighbouring neurons is shunted, while correlated input is not.
Reference:
1 . Hjorth J, Blackwell KT, Kotaleski JH (2009) Gap junctions between striatal fast-spiking interneurons regulate spiking activity and synchronization as a function of cortical activity. J Neurosci 29:5276-86 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell; Synapse; Channel/Receptor; Dendrite;
Brain Region(s)/Organism: Basal ganglia;
Cell Type(s): Neostriatum fast spiking interneuron;
Channel(s): I A; I_K,Na;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Activity Patterns; Ion Channel Kinetics; Synchronization; Detailed Neuronal Models;
Implementer(s): Hjorth, Johannes [hjorth at csc.kth.se];
Search NeuronDB for information about:  I A; I_K,Na; Gaba; Glutamate;
% Sets up and runs the fsNetwork simulation
% The neuron have different slightly randomized cell parameters
%
% This code is to test if higher input frequency means a relative
% lower decrease of firing frequency due to gap junctions
%
% 
% To generate Figure 6A:
%
% runTenFShigherFreqLessShunting.m
% readHigherFreqLessShuntingData.m
% makeHigherFreqLessShuntingPlot.m
%
%

clear all, format compact
tic

% Matlab helper scripts are located here
path(path,'../matlabScripts')

% Genesis model is located here
path(path,'../genesisScripts')

nReps = 10 % 10 % 10 

corrRudolph = 0.5;

upFreqVector = linspace(1,10,10);
%upFreq = 20/9; %10/9 
noiseFreq = 1/9;
maxTime = 10 % 10 % 100 
allowVar = 1 % 0

numCells = 10;
numGJ = 3;  % 3*10/2 = 15, 10*9/2 = 45, 15/45 = 1/3 = 33 % coupling
            % Also try with numGJ = 4 ---> 44% coupling

channelMask = {'A_channel'} % Lägg till fler om fler ska varieras
cellVar = 0.5 % 0.2 % 0.1;
lenVar = 0.5 % 0.2 %0.1;



dataFile{1} = 'TenInhomoFS-prim-AllUpstate-HigherFreqLessShunt';
dataFile{2} = 'TenInhomoFS-nonConRef-AllUpstate-HigherFreqLessShunt';


dataDir = 'UTDATA/SAVED/TenFS-higherFreqLessShunt/';

for rep=1:nReps

  disp('Pausing for 3 seconds, press Ctrl+C to abort')
  pause(3)
    
  randSeed = floor(sum(clock)*1e5);

  % Generate network connections
  clear gapSrc gapDest
  [gapSrc, gapDest, conMat] = makeFSrandomNetwork(numCells,numGJ);
  %  figure, showFSnetwork(conMat, randSeed)

  conMatFile = strcat([dataDir 'conMat-' num2str(randSeed)], '.mat');
  save(conMatFile, 'conMat');
    
  gapSource{1} = gapSrc;
  gapSource{2} = []; % Reference case
  gapDest{1} = gapDest;
  gapDest{2} = []; % Reference case

  gapIdNonCon = 2;
    
  % 2e9 ohm = 0.5nS
  primGapRes = ones(length(gapSrc),1)*2e9 

  clear gapRes
    
  gapRes{1} = primGapRes;
  gapRes{2} = inf; % Reference case, unconnected

  % Generera FS morphologin
  makeFSMorph(numCells, cellVar, channelMask, lenVar)

  % Generate input!
    
  for freqIdx = 1:length(upFreqVector)
    upFreq = upFreqVector(freqIdx);
    

    % Only upstate input
    makeAllExternalInputAllUpstate(corrRudolph, upFreq, noiseFreq, ...
                                   max(maxTime,100), allowVar, ...
                                   randSeed, numCells);

    
    
    % Loopa två varv, ett för prim och ett för okopplat
    
    for gapIdx = 1:length(gapRes)

      disp('Pausing for 1 second, press Ctrl+C to abort')
      pause(1)

        
      writeParameters(maxTime,numCells, ...
                      gapSource{gapIdx}, gapDest{gapIdx}, gapRes{gapIdx}, ...
                      dataFile{gapIdx});

                       
                    
                    
      system('genesis ../genesisScripts/simFsMultiInhomogene');

      %% Save data
        
      saveFileData = [dataDir dataFile{gapIdx} ...
                      '-id' num2str(randSeed) ...
                      '-gapres-' num2str(gapRes{gapIdx}(1)) ...
                      '-upFreq-' num2str(upFreq) ...
                      '.data'];
                
      saveFileInfo = strrep(saveFileData,'.data','.info');

        
      system(['cp UTDATA/' dataFile{gapIdx} '.data ' saveFileData]);
        
      system(['cp INDATA/parameters.txt ' saveFileInfo]);
      system(['cat INDATA/inputInfo.txt >> ' saveFileInfo]);

    end
  end    
end

%% Add code to generate figures here

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