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

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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]
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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.2

clear all

global  beta gamma delta Em0 cumul Ac maxAc Eml1 
S = [0    -1     
     0    -1 ];
R = [0    1  ];
groupex=find(sum(S)>=0);
groupin=find(sum(S)<0); 
Ne=length(groupex);     Ni=length(groupin);
retards=ones(Ne+Ni);
th=[0.5*ones(Ne,1); 	0.5*ones(Ni,1)];

modul=1;            %l1 automodulation if modul=1      
epsilon=0.06;       %dynamical noise
beta=1.05 ;          
gamma=0;            %modulation noise
maxAc=6;            
delta=0;            %noise on maxAc     
Em0=0.1;              
vseuiL=[1];
seedscalevol=5;randn('seed',seedscalevol) ;    rand('seed',seedscalevol);
Tsim=150;
Init=zeros(Ne+Ni,1);
type=(sign(sum(S)))';
nirings=[zeros(sum(Init),1),find(Init==1),type((Init==1))];
hstock=zeros(Ni+Ne,Tsim);
hstock(:,1)=Init;
matact=zeros(Ni+Ne,Tsim);
matact(:,1)=Init;
Ac=0;                   %l1 spike counter
Eml1=0;                 %l1 automodulation initialization 
retL=1;                 %l1 postsynaptic delay
%*****************************
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

         if ~isempty(feu)                                           
            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=S.*matfiltre;                           
                h=h+sum(Sfiltre(:,firedtone),2);  
          end
         else
             h=R';
        end
       inter1=find(nirings(:,1)==t-retL);   
       finter1=[nirings(inter1,2)];
       finter2=[nirings(inter1,1)];
       lfire=(sum(finter1==1)>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)];                 
  end
end



% Create figure
figure1 = figure('PaperType','a4letter','PaperSize',[20.98 29.68],...
    'Color',[1 1 1]);
% Create rectangle
annotation(figure1,'rectangle','FaceColor',[0 0 0],...
    'Position',[0.2786 0.7476 0.04 0.04]);
% Create line
annotation(figure1,'line',[0.2186 0.2286],[0.8976 0.8776],'LineWidth',0.6);
% Create line
annotation(figure1,'line',[0.2286 0.2186],[0.8776 0.8576],'LineWidth',0.6);
% Create line
annotation(figure1,'line',[0.1886 0.2186],[0.8976 0.8976],'LineWidth',0.6);
% Create line
annotation(figure1,'line',[0.2186 0.1886],[0.8576 0.8576],'LineWidth',0.6);
% Create line
annotation(figure1,'line',[0.1886 0.1786],[0.8576 0.8776],'LineWidth',0.6);
% Create line
annotation(figure1,'line',[0.1786 0.1886],[0.8776 0.8976],'LineWidth',0.6);
% Create arrow
annotation(figure1,'arrow',[0.2286 0.3336],[0.8776 0.8776],'HeadLength',7,...
    'HeadWidth',7,...
    'LineStyle','--');
% Create arrow
annotation(figure1,'arrow',[0.2686 0.2786],[0.7676 0.7676],'HeadLength',7,...
    'HeadWidth',7);
% Create arrow
annotation(figure1,'arrow',[0.2858 0.2686],[0.6676 0.6676],'HeadLength',7,...
    'HeadWidth',7);
% Create rectangle
annotation(figure1,'rectangle','LineStyle','--','FaceColor','flat',...
    'Position',[0.1786 0.6676 0.12 0.1]);
% Create rectangle
annotation(figure1,'rectangle','FaceColor',[1 1 1],...
    'Position',[0.1886 0.6376 0.08 0.06]);
% Create textbox
annotation(figure1,'textbox','String','Mod','FontWeight','bold',...
    'FontSize',9,...
    'FontName','Arial',...
    'FontAngle','italic',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.1886 0.6976 0 0.008]);
% Create arrow
annotation(figure1,'arrow',[0.3386 0.2986],[0.8676 0.7876],'HeadLength',7,...
    'HeadWidth',7,...
    'Color',[0.5 0.5 0.5]);
% Create textbox
annotation(figure1,'textbox','String',{'E'},'FontWeight','bold',...
    'FontSize',9,...
    'FontName','Arial',...
    'FontAngle','italic',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.1886 0.9476 0.004 0.001]);
% Create arrow
annotation(figure1,'arrow',[0.3836 0.3736],[0.9076 0.8976],'HeadLength',7,...
    'HeadWidth',7,...
    'Color',[0.5 0.5 0.5]);
% Create textbox
annotation(figure1,'textbox','String',{'l1'},'FontWeight','bold',...
    'FontName','Arial',...
    'FontAngle','italic',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.3186 0.8176 0.001 0.001]);
% Create textbox
annotation(figure1,'textbox','String',{'l2'},'FontWeight','bold',...
    'FontName','Arial',...
    'FontAngle','italic',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.3586 0.8676 0.001 0.001],...
    'Color',[0.5 0.5 0.5]);
% Create ellipse
annotation(figure1,'ellipse','Position',[0.3286 0.8876 0.06 0.07],...
    'Color',[0.5 0.5 0.5]);
% Create ellipse
annotation(figure1,'ellipse','FaceColor',[0.5 0.5 0.5],...
    'Position',[0.3336 0.8576 0.05 0.05],...
    'Color',[0.5 0.5 0.5]);
% Create textbox
annotation(figure1,'textbox','String',{'A'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.005 0.85 0.004 0.001]);
% Create textbox
annotation(figure1,'textbox','String',{'B'},'FontSize',16,...
    'FontName','Arial',...
    'FitHeightToText','off',...
    'EdgeColor',[1 1 1],...
    'Position',[0.005 0.2262 0.004 0.001]);
%figure (1) 
plot(Eml1,'LineWidth',1,'Color',[0 0 0])


set(gca,'XTick',[0: Tsim/3: Tsim])
text(-13,2.5,['Em'],'FontWeight','bold','FontSize',10,'FontAngle','italic')
text(-5,2.4,['l1'],'FontWeight','bold','FontSize',9,'FontAngle','italic')
text(105,3.85,['max'],...  
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...
    'FontName','arial','FontWeight','normal','FontSize',12,'FontAngle','italic')
hold on
%set(gca,'YTickLabel',[])
set(gca,'FontName','arial','FontWeight','bold','FontSize',10)
plot(Ac/(2*max(Ac))-1,'LineWidth',0.5,'Color',[0 0 0])
set(gca,'XTick',[0: Tsim/3: Tsim])
set(gca,'XTickLabel',[0 5 10 15]);
set(gca,'YTickLabel',{'0' '6' '0' '0.5' '1' '1.5' '2' ''});
hold on
set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
xlabel('time (s)');
line([10 length(Eml1)],[-0.2 -0.2],'LineWidth',0.5,'Color',[0.5 0.5 0.5], 'LineStyle',':')
plot(nirings((nirings(:,2)==1),1), nirings((nirings(:,2)==1),2)-1.2,'diamond','MarkerEdgeColor',[0 0 0],'MarkerFaceColor',[0 0 0], 'MarkerSize', 2)
set(gca,'XTick',[0: Tsim/3: Tsim])
set(gca,'LineWidth',0.2)

set(gca,'FontName','arial','FontWeight','bold','FontSize',9)
reperexmax=find(Eml1==max(Eml1));
reperexmax=reperexmax(1);
repxmax=find(Ac==max(Ac));
for i=1:length(repxmax)
line(repxmax(i)*ones(1,2),[-1 0.5],'LineWidth',1,'Color',[0 0 0], 'LineStyle','-.')
end
line([0,Tsim],zeros(1,2),'LineWidth',0.2,'Color',[0 0 0], 'LineStyle','-')
line([0,0.00001],[-0.01,-0.499],'LineWidth',20,'Color',[1 1 1], 'LineStyle','-')


text(65,-0.5,...
     '\leftarrowMaxAc',...
     'FontName','arial','FontWeight','normal','FontSize',10,'FontAngle','italic')
 text(5,0.1,...
     '\leftarrow-----Emo',...
     'FontName','arial','FontWeight','normal','FontSize',10,'FontAngle','italic')
text(-13, -0.5,[' Ac'],...
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...
    'FontName','arial','FontWeight','bold','FontSize',10,'FontAngle','italic' )
text(80,0.7,[' b'],...  
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...
    'FontName','symbol','FontWeight','bold','FontSize',12,'FontAngle','italic')
text(-18,-0.2,[' l1 firings '],...  
    'VerticalAlignment','middle',...
    'HorizontalAlignment','left',...
    'FontName','arial','FontWeight','bold','FontSize',9,'FontAngle','italic')
box off
set(gcf,'Color',[1 1 1],'position',[100 100 520 420]);