Neural model of frog ventilatory rhythmogenesis (Horcholle-Bossavit and Quenet 2009)

 Download zip file 
Help downloading and running models
Accession:123987
"In the adult frog respiratory system, periods of rhythmic movements of the buccal floor are interspersed by lung ventilation episodes. The ventilatory activity results from the interaction of two hypothesized oscillators in the brainstem. Here, we model these oscillators with two coupled neural networks, whose co-activation results in the emergence of new dynamics. .. The biological interest of this formal model is illustrated by the persistence of the relevant dynamical features when perturbations are introduced in the model, i.e. dynamic noises and architecture modifications. The implementation of the networks with clock-driven continuous time neurones provides simulations with physiological time scales."
Reference:
1 . Horcholle-Bossavit G, Quenet B (2009) Neural model of frog ventilatory rhythmogenesis. Biosystems 97:35-43 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s): Temporal Pattern Generation; Oscillations; Synchronization;
Implementer(s):
%Biosystems. 2009 Jul;97(1):35-43.
%Horcholle-Bossavit G, Quenet B.
%Neural model of frog ventilatory rhythmogenesis.
%Fig.7
clear all

global beta gamma maxAc delta Em0 cumul  Ac  Eml1

germe=18   ;
facteur=0.15;
nombrerreur= 60;
matdep =[ 0  0  -1   
          1  0  -1   
          0  1  0 ];                      
Rdep=[1 0 0 ]; 
matL=[0 -1 0 ; 0 -1 0; 0 0 0];
X=6;
Y=2;
mattoub=boucladj(matdep,Rdep', X, [4,2],1, [2,5], -1);  
Spre=mattoub(:,1:end-1);
Rpre=mattoub(:,end);
Spara=bouclpara(Spre,Rpre, Y); 
R=Spara(:,end);
S=Spara(:,1:end-1);
R=R';
vectv=zeros(size(S,1),1);
vectv([1:Y*(1+X*2)])=1;
vecth=zeros(1, size(S,2));
inhibsl=[];
for y=1:Y
    inhibsl=[inhibsl, [0:X-1]*2+3+(y-1)*((X*2)+1)];
end
inhibsl;
vecth(inhibsl)=-1;
excitateurs=[1,[1:X]*2];
for y=2:Y
    excitateursy=[1+(y-1)*((X*2)+1),[1:X]*2+(y-1)*((X*2)+1)];
    excitateurs=[excitateurs;excitateursy];
end
excitateurs;
taillantiphase=2;
groupebc=[ ];
groupebd=[ ];
for i=1:size(excitateurs,2)
    if mod(floor((i-1)/taillantiphase),2)==0
        groupebc=[groupebc,excitateurs(1,i)];
    else
        groupebd=[groupebd,excitateurs(1,i)];
    end
end
groupebc=groupebc(2:end);

for y=2:Y
    groupebcy=[ ];
    groupebdy=[ ];
    for i=1:size(excitateurs,2)
        if mod(floor((i-1)/taillantiphase),2)==0
            groupebcy=[groupebcy,excitateurs(y,i)];
        else
            groupebdy=[groupebdy,excitateurs(y,i)];
        end
    end
    groupebc=[groupebc,groupebcy(2:end)];
    groupebd=[groupebd,groupebdy];
end
groupebdin=groupebd+1;                  
vectv(groupebd)=1;                      
vectv(groupebdin)=0;           
S=completelop(matL,vectv,vecth,S,1);
R=[0 1 0,R];
inhibsl=inhibsl+3;
excitateurs=excitateurs+3;
groupebc=groupebc+3;
groupebd=groupebd+3;
groupebdin=groupebdin+3;
excitateurs=excitateurs(:,2:end);
excitateurs=reshape(excitateurs',1,size(excitateurs,1)*size(excitateurs,2));
v=1:Y;
for i=1:X
    for j=1:Y
        for k=1:Y
            S(excitateurs((k-1)*X+i),inhibsl((j-1)*X+i))=-1;
        end
    end
end

S1=matmodif(S,nombrerreur,facteur,germe);
B=nnz(S1);
groupex=find(sum(S1)>=0);
groupin=find(sum(S1)<0); 
Ne=length(groupex);
Ni=length(groupin);
Ne=length(groupex);     Ni=length(groupin);
retards=ones(Ne+Ni);
th=[0.5*ones(Ne,1); 	0.5*ones(Ni,1)];

modul=1;        
epsilon=0.15;              
beta=1.07 ;            
gamma=0.2 ;             
delta=6;
maxAc=6;
Em0=0.1;


vseuiL=[1;zeros(Ne+Ni-1,1)];   

seedscalevol=1;
randn('seed',seedscalevol)     
rand('seed',seedscalevol)

%initialisations 
Init=zeros(Ne+Ni,1);
type=(sign(sum(S1)))';
groupe=zeros(size(S1,1),1);
groupe(1)=3; 
Tsim=150;            
groupe(groupebc)=1;
groupe(groupebd)=2;
nirings=[zeros(sum(Init),1),find(Init==1),type((Init==1)),groupe((Init==1))];
hstock=zeros(Ne+Ni,Tsim);
hstock(:,1)=Init;
matact=zeros(Ne+Ni,Tsim);
matact(:,1)=Init;
Ac=0;
Eml1=0;
retL=1;   
%*****************************
delaiaff=0;
finaff=Tsim;
Tomax=max(max(retards));
cumul=0;
for t=1:Tsim
    feu=[];
    matfiltre=zeros(Ne+Ni);
    h=R';
    if ~isempty(nirings)
       for ret=1:max(max(retards))
           fincre=zeros(Ne+Ni);                           
           inter=find(nirings(:,1)==t-ret);               
           feu=[feu; ret+0*inter,inter];                  
           finter=[[nirings(inter,2)]', Ne+Ni+1];          
           fincre(1:Ne+Ni,finter)=1;                       
           fincre=fincre(:,1:Ne+Ni);                       
           matinter=(retards==ret);                        
           matfiltre=matfiltre+((matinter==fincre)&(matinter>0));   
       end
       tfire=nirings(feu(:,2),1);                          
       firedt=nirings(feu(:,2),2);                         
       st=sort(firedt); 
       
       if ~isempty(st)                                   
           dst=diff(st);                                   
           y=st(dst>0);
           firedtone=[y;st(end)];                          
           Sfiltre=S1.*matfiltre;                           
           h=h+sum(Sfiltre(:,firedtone),2);  
       end
       inter1=find(nirings(:,1)==t-retL);   
         finter1=[nirings(inter1,2)];
         finter2=[nirings(inter1,1)];
         l1fire=(sum(finter1==1)>0);  
         lfire=(l1fire>0);
         modulation(lfire);
    end
    randh=randn(Ne+Ni,1);

    hent=h+Eml1(end)*(modul==1)*vseuiL+epsilon*randh-th;                                                            
    hstock(:,t+1)=hent;
    n=(hent>0);                                                
    fired=find(n>0);
    matact(:,t+1)=n;
    
    if ~isempty(fired);
        nirings=[nirings; t+0*fired,fired,type(fired),groupe(fired)];                 
    end
   
end

matactbc=matact(groupebc,:);
matactbd=matact(groupebd,:);
matactl=matact(1,:);
actot=sum(matact(groupex(2:end),:));
actotin=sum(matact(groupin,:));
     indexc1=find(nirings(:,4)==1 & nirings(:,1));
     indexd1=find(nirings(:,4)==2 & nirings(:,1));
     indexl1=find(nirings(:,4)==3 & nirings(:,1)) ;

figure
set(gcf,'Color',[1 1 1])    

set(gca,'XTickLabel',[])
subplot('position',[0.12 0.68 0.28 0.28]);
imagesc(S);
 set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
notremap=[1 0 0;1 1 1;0 0 1];
colormap(flipud(notremap))
notremap=[0 0 0;1 1 1;0.5 0.5 0.5];
colormap(flipud(notremap))
subplot('position',[0.55 0.68 0.28 0.28]);

imagesc(S1, [-1 1] );
 set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
notremap=[0.5 0.5 0.5; repmat([0.85 0.85 0.85],8,1) ;1 1 1;repmat([0.85 0.85 0.85],8,1) ; 0 0 0];
colormap(notremap)
text(-55,1,['A'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','normal','FontSize',16,'FontAngle','normal','Color',[0 0 0])
text(-52,10,['a'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','normal','FontSize',16,'FontAngle','normal','Color',[0 0 0])
text(-8,10,['b'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','normal','FontSize',16,'FontAngle','normal','Color',[0 0 0])
subplot('position',[0.08 0.28 0.85 0.30])
plot(nirings(indexl1,1),nirings(indexl1,2),'diamond','MarkerEdgeColor',[0 0 0],'MarkerFaceColor',[0 0 0], 'MarkerSize', 1 )
 hold on
plot(nirings(indexc1,1),nirings(indexc1,2),'diamond','MarkerEdgeColor',[0 0 0],'MarkerFaceColor',[0 0 0], 'MarkerSize', 1 )
plot(nirings(indexd1,1),nirings(indexd1,2),'diamond','MarkerEdgeColor',[0.5 0.5 0.5],'MarkerFaceColor',[0.5 0.5 0.5], 'MarkerSize', 1 )
hold off
     set(gca,'YLim',[0 Ne+Ni+1]);
     set(gca,'YDir','reverse')
     set(gca,'XLim',[0 Tsim]);
     set(gca,'XTick',[0: Tsim/4: Tsim])
     set(gca,'XTickLabel',[])
     set(gca,'FontName','arial','FontWeight','bold','FontSize',10)
 text(-12,5,['B'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','normal','FontSize',16,'FontAngle','normal','Color',[0 0 0])
text(5,-2,['excitatory neurone activities'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','normal','Color',[0 0 0])    
     actot=sum(matact(groupex(1:end),:));
     actotbc1=sum(matact([1 groupebc],:));
     actotbd1=sum(matact(groupebd,:));
    
    box off
subplot('position',[0.08 0.09 0.85 0.14])
     plot(actotbc1,'LineWidth',0.5,'Color',[0 0 0], 'LineStyle','-');
     hold on
     plot(actotbd1,'LineWidth',0.5,'Color',[0.5 0.5 0.5], 'LineStyle','-');
     hold off
     set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
set(gca,'XLim', [0 Tsim],'YLim',[0  10]);
set(gca,'XTickLabel',[0 5 10 15])
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
xlabel('time (s)');
 box off
     text(37,4.5,['Bc'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',8,'FontAngle','italic','Color',[0 0 0])
text(77,4.5,['Bd'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',8,'FontAngle','italic','Color',[0.5 0.5 0.5])

text(5,11,['number of active Bc and Bd neurones'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','normal','Color',[0 0 0]) 
text(30,5,['OS'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','italic','Color',[0 0 0]) 
text(70,5,['OS'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','italic','Color',[0.5 0.5 0.5]) 
 text(-12,7,['C'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...     
    'FontName','arial','FontWeight','normal','FontSize',16,'FontAngle','normal','Color',[0 0 0])
box off
set(gcf,'Color',[1 1 1],'position',[100 100 520 420]);