Maincounter.m

From 2006.igem.org

clear all;
close all; 
 

%default:
% n  = 3;
% nSa  = 3;
% nSr  = 3;
% K  = 5;
% KSa  = 5;
% KSr  = 5;
% k  = 2;
% kd  = 1;
% period = 30;

n  = 1;  % keine Kooperativität der Zinkfinger -> alle n immer = 1
nSa  = 3; % Kooperativität von S (als Aktivator)
nSr  = 3; % Kooperativität von S (als Repressor)
K  = 120; % Affinität (höheres K = höhere Affinität)
KSa  = 5;
KSr  = 5;
k  = 2;
kd  = 0.9; % Degradationsrate der Zinkfinger

para = [n,nSa,nSr,K,KSa,KSr,k,kd,period];
y0 = [2,0,0,0];
opt = odeset('RelTol',1e-3,'AbsTol',1e-6); 

% stepsize
tstep = 0.2;
% duration
tfinal = 600;

% run computation
[t,y] = ode15s('ode_counter',[0:tstep:tfinal],y0,opt,para);

s = input_signal([0:tstep:tfinal],period);

%plot 4 concentrations plus S over time
colors = ['k' 'm' 'c' 'g' 'r'];
%colors = ['k' 'k' 'k' 'k' 'k']; %for doing powerpoint presentations
for i = 1:4,
   subplot(5,1,i);
   plot(t,y(:,i),colors(i));
   axis([0 tfinal -0.1 2.1]);
   ylabel(sprintf('[R%d]', i))
   hold on; 
end
subplot(5,1,5);
plot(t,s,colors(5));
axis([0 tfinal -0.1 1.1]);
ylabel('[S]')
xlabel('time')

hold off;

param=[K, kd];
v = jury(y, [0:tstep:tfinal], period, tstep, tfinal, param);