% Create randomized connections among neurons in the 5 CCTC loops
% Author: Xu Zhang @UConn, Apr., 2019
clear;clc;
% Initialize rng seed
rngSEED = ceil(rand*899+100);
rng(rngSEED);
disp(rngSEED);
%% ION gap junctions
subGroupMat = [0 1 1 0 1 0 0 0;1 0 0 1 0 1 0 0;1 0 0 1 0 0 1 0;0 1 1 0 0 0 0 1;1 0 0 0 0 1 1 0;0 1 0 0 1 0 0 1;0 0 1 0 1 0 0 1;0 0 0 1 0 1 1 0];
IONgapmat = blkdiag(subGroupMat,subGroupMat,subGroupMat,subGroupMat,subGroupMat);
for i = 11:15
IONgapmat(rem(i-1,5)*8+1,rem(i-2,5)*8+2)=1;
IONgapmat(rem(i-1,5)*8+2,rem(i,5)*8+1)=1;
IONgapmat(rem(i-1,5)*8+3,rem(i-2,5)*8+4)=1;
IONgapmat(rem(i-1,5)*8+4,rem(i,5)*8+3)=1;
end
% IONgapmat is the connectivity matrix within ION cells
IONgap_all = [];
for i = 1:size(IONgapmat,1)
IONgap_all = [IONgap_all;find(IONgapmat(i,:)==1)'];
end
% Set gap junction connectivity
formatSpec = '%d \n';
PYNint_fileID = fopen('params_ION_gapj.txt','w');
fprintf(PYNint_fileID,formatSpec,length(IONgap_all));
fprintf(PYNint_fileID,formatSpec,sum(IONgapmat,2));
fprintf(PYNint_fileID,formatSpec,IONgap_all);
fclose(PYNint_fileID);
% Set gap junction conductance
formatSpec = '%.4f \n';
ION_gapstrength = rand(length(IONgap_all),1)*0.4+0.3;
IONgaps_fileID = fopen('params_ION_gapstrength.txt','w');
fprintf(IONgaps_fileID,formatSpec,ION_gapstrength);
fclose(IONgaps_fileID);
% Set offset currents to ION
formatSpec = '%.4f \n';
ION_oc = 1e-3*(randn(40,1)*0.02-1.3);
IONoc_fileID = fopen('params_ION_oc.txt','w');
fprintf(IONoc_fileID,formatSpec,ION_oc);
fclose(IONoc_fileID);
%% PYN connections
modelscale = 5; % 5 loops
width = 2.5; PYNintmat = tril(triu(true(20*modelscale),-ceil(width)),floor(width))-diag(true(20*modelscale,1));
for i=1:ceil(width)
PYNintmat(i,end-ceil(width)+i:end) = true; PYNintmat(end-floor(width)+i:end,i) = true;
end
% PYNintmat is the connectivity matrix within PYN cells
PYNint_all = [];
for i = 1:length(PYNintmat)
PYNint_all = [PYNint_all;find(PYNintmat(i,:)==1)'];
end
formatSpec = '%d \n';
PYNint_fileID = fopen('params_PY_int.txt','w');
fprintf(PYNint_fileID,formatSpec,length(PYNint_all));
fprintf(PYNint_fileID,formatSpec,PYNint_all);
fclose(PYNint_fileID);
%% ION-PC connections
% Randomized connections with constraints, see SI Note 3 2)
IONPCmat = zeros(40,200);
groupRatioIONPC = round(randn(4,1)*4+40);
groupRatioIONPC(5) = 200-sum(groupRatioIONPC(1:4));
while min(groupRatioIONPC)<=30 || max(groupRatioIONPC)>=50 || length(find(groupRatioIONPC>40))>=4 || length(find(groupRatioIONPC<40))>=4
groupRatioIONPC = round(randn(4,1)*4+40);
groupRatioIONPC(5) = 200-sum(groupRatioIONPC(1:4));
end
IONPCcount = 0;
for m = 1:5
subRatioIONPC = abs(round(randn(7,1)*2+5));
subRatioIONPC(8) = groupRatioIONPC(m)-sum(subRatioIONPC(1:7));
while min(subRatioIONPC)<=1 || max(subRatioIONPC)>=10 || length(find(subRatioIONPC>=7))>=6 || length(find(subRatioIONPC<=3))>=6
subRatioIONPC = abs(round(randn(7,1)*2+5));
subRatioIONPC(8) = groupRatioIONPC(m)-sum(subRatioIONPC(1:7));
end
for n = 1:8
IONPCmat((m-1)*8+n,(IONPCcount+1):(IONPCcount+subRatioIONPC(n))) = 1;
IONPCcount = IONPCcount + subRatioIONPC(n);
end
end
% IONPCmat is the connectivity matrix between ION->PC
IONPC_all = [];
for i = 1:size(IONPCmat,1)
IONPC_all = [IONPC_all;find(IONPCmat(i,:)==1)'];
end
formatSpec = '%d \n';
PYNint_fileID = fopen('params_ION2PC.txt','w');
fprintf(PYNint_fileID,formatSpec,sum(IONPCmat,2));
fprintf(PYNint_fileID,formatSpec,IONPC_all);
fclose(PYNint_fileID);
%% PC-DCN connections
% Randomized connections with constraints, see SI Note 3 3)
groupPCDCN = round(randn(4,1)*4+40);
groupPCDCN(5) = 200-sum(groupPCDCN(1:4));
while min(groupPCDCN)<=30 || max(groupPCDCN)>=50 || length(find(groupPCDCN>40))>=4 || length(find(groupPCDCN<40))>=4
groupPCDCN = round(randn(4,1)*4+40);
groupPCDCN(5) = 200-sum(groupPCDCN(1:4));
end
PCDCNmat = zeros(200,5);
PCDCNcount = 0;
for m = 1:5
PCDCNmat((PCDCNcount+1):(PCDCNcount+groupPCDCN(m)),m) = 1;
PCDCNcount = PCDCNcount + groupPCDCN(m);
end
% PCDCNmat is the connectivity matrix between PC->DCN
PCDCN_all = [];
for i = 1:size(PCDCNmat,1)
PCDCN_all = [PCDCN_all;find(PCDCNmat(i,:)==1)'];
end
formatSpec = '%d \n';
PYNint_fileID = fopen('params_PC2DCN.txt','w');
fprintf(PYNint_fileID,formatSpec,sum(PCDCNmat,2));
fprintf(PYNint_fileID,formatSpec,PCDCN_all);
fclose(PYNint_fileID);
%% DCN-ION connections
% Randomized connections with constraints, see SI Note 3 4)
groupRatioDCNION = round(randn(4,1)*4+8);
groupRatioDCNION(5) = 40-sum(groupRatioDCNION(1:4));
while min(groupRatioDCNION)<=4 || max(groupRatioDCNION)>=12 || length(find(groupRatioDCNION>8))>=4 || length(find(groupRatioDCNION<8))>=4
groupRatioDCNION = round(randn(4,1)*4+8);
groupRatioDCNION(5) = 40-sum(groupRatioDCNION(1:4));
end
DCNIONcount = 0;
currentIONlist = 1:40;
DCNIONmat = zeros(5,40);
for m = 1:4
tmprange = length(currentIONlist);
tmpIONind = ceil(rand(groupRatioDCNION(m),1)*(tmprange-1))+1;
while length(unique(tmpIONind))<length(tmpIONind)
tmpIONind = ceil(rand(groupRatioDCNION(m),1)*(tmprange-1))+1;
end
DCNIONmat(m,currentIONlist(tmpIONind)) = 1;
currentIONlist(tmpIONind)=[];
end
DCNIONmat(5,currentIONlist) = 1;
% DCNIONmat is the connectivity matrix between DCN->ION
DCNION_all = [];
for i = 1:size(DCNIONmat,1)
DCNION_all = [DCNION_all;find(DCNIONmat(i,:)==1)'];
end
formatSpec = '%d \n';
PYNint_fileID = fopen('params_DCN2ION.txt','w');
fprintf(PYNint_fileID,formatSpec,sum(DCNIONmat,2));
fprintf(PYNint_fileID,formatSpec,DCNION_all);
fclose(PYNint_fileID);