Ode counter.m

From 2006.igem.org

function varargout = ode_counter(t,y,flag,para)

switch flag
    case ' '
        
        % parameter values    
        
        n  = para(1); % Kooperativität der Zinkfinger
        nSa  = para(2); % Kooperativität von S (als Aktivator)
        nSr  = para(3); % Kooperativität von S (als Repressor)
        K  = para(4); % Affinität (höheres K = höhere Affinität)
        KSa  = para(5);
        KSr  = para(6);
        k  = para(7); 
        kd  = para(8); % Degradationsrate der Zinkfinger
        period = para(9);
        
        % input signal
        S = input_signal(t,period);
        
        % calculate RHS states
        
        % product of act and rep, respectively, since the "roadblocks" (mechanical obstacle) are
        % in succession (probabilities multiplied)
        % Joerg roughly agrees.
         dy1 = [k * act(S,KSa,nSa) * rep(y(2),K,n) * rep(y(3),K,n) - kd * y(1)]; 
         dy2 = [k * rep(S,KSr,nSr) * rep(y(3),K,n) * rep(y(4),K,n) - kd * y(2)]; 
         dy3 = [k * act(S,KSa,nSa) * rep(y(4),K,n) * rep(y(1),K,n) - kd * y(3)]; 
         dy4 = [k * rep(S,KSr,nSr) * rep(y(1),K,n) * rep(y(2),K,n) - kd * y(4)];
        
        % pack to array
        dy = [dy1;dy2;dy3;dy4];
        
        % assign output
        varargout{1} = dy;
        
    case 'init'
        
        y0 = y;
       
    otherwise
        error(['Unknown flag  flag .']);
       
end

return