how to solve the below error

Undefined function or variable 'm1'.

Error in repressilator (line 7) y = [m1 p1 m2 p2 m3 p3];

in matlab program function ydot=repressilator(t,y,p) alpha0 = 1; n = 2.0; beta = 5; alpha = 1000; % order of species; y = [m1 p1 m2 p2 m3 p3]; m1 = -y(1) + alpha/(1+y(6)^n) + alpha0; p1 = -beta*(y(2) - y(1)); m2 = -y(3) + alpha/(1+y(2)^n) + alpha0; p2 = -beta*(y(4) - y(3)); m3 = -y(5) + alpha/(1+y(4)^n) + alpha0; p3 = -beta*(y(6) - y(5)); ydot = [m1; p1; m2; p2; m3; p3]; timespan=[0 15]; y0 = [0 1 0 1 0 1]; [t,y] = ode45(@repressilator,timespan,y0); figure() plot(t,y) xlabel('Time') ylabel('Amount') legend('m1','p1','m2','p2','m3','p3','Location','SouthEast') figure() plot(y(:,1), y(:,2)) xlabel('Amount m1') ylabel('Amount p1')

Answer 1

[Torsten]

function main
timespan=[0 15];
y0 = [0 1 0 1 0 1];
[t,y] = ode45(@repressilator,timespan,y0); 
figure()
plot(t,y)
xlabel('Time')
ylabel('Amount')
legend('m1','p1','m2','p2','m3','p3','Location','SouthEast')
figure()
plot(y(:,1), y(:,2)) 
xlabel('Amount m1')
ylabel('Amount p1')
end

function ydot=repressilator(t,y)
    alpha0 = 1;
    n = 2.0;
    beta = 5;
    alpha = 1000;
    % order of species;
    m1 = -y(1) + alpha/(1+y(6)^n) + alpha0;
    p1 = -beta*(y(2) - y(1));
    m2 = -y(3) + alpha/(1+y(2)^n) + alpha0;
    p2 = -beta*(y(4) - y(3));
    m3 = -y(5) + alpha/(1+y(4)^n) + alpha0;
    p3 = -beta*(y(6) - y(5));
    ydot = [m1; p1; m2; p2; m3; p3];
end

[Dev]

HOW TO SOLVE THE BELOW ERROR Undefined function or variable 'repressilatorddt'.

Error in odearguments (line 90) f0 = feval(ode,t0,y0,args{:}); % ODE15I sets args{1} to yp0.

Error in ode45 (line 115) odearguments(FcnHandlesUsed, solver_name, ode, tspan, y0, options, varargin);

Error in repressilatorr (line 31) [t,s]=ode45(ODEFUN, [0,Tend], x0, options);

IN PROGRAM %file repressilator.m %Model of repressilator oscillatory genetic circuit %from Elowitz and Leibler (2000) Nature 403, pp 335-338. %Figure 7.21

function repressilatorr

clear all

%declare model parameters global alpha global alpha0 global n global beta

%assign parameter values alpha0=60*(5e-4); %transcripts/sec alpha=60*(5-alpha0); %transcripts/sec n=2; beta=1/5;

%set simulation parameters Tend=1000 ODEFUN=@repressilatorddt; options=odeset('Refine', 6);

%set initial condition: state = [m1 p1 m2 p2 m3 p3] x0=[0.2 0.1, 0.3 0.1 0.4 0.5]';

%run simulation [t,s]=ode45(ODEFUN, [0,Tend], x0, options);

%produce figure 7.21A figure(1) set(gca,'fontsize',14) t=t/0.3485 plot(t,40*s(:,2), 'k',t,40*s(:,4), 'k--', t,40*s(:,6), 'k:','Linewidth', 3) axis([0 800 0 7000]) ylabel('protein abundance (molecules per cell)') xlabel('Time (min)') legend('Protein 1', 'Protein 2', 'Protein 3')

Answer 2

[Ankita Bansal]

Hi DEVI, are you trying to run this example?

You have written ODEFUN=@repressilatorddt; but you have not defined repressilatorddt.

You can modify your code to

function repressilatorr

clear all

%declare model parameters
global alpha 
global alpha0 
global n 
global beta

%assign parameter values 
alpha0=60*(5e-4); %transcripts/sec 
alpha=60*(5-alpha0); %transcripts/sec 
n=2; 
beta=1/5;

%set simulation parameters 
Tend=1000
ODEFUN=@repressilatorddt; 
options=odeset('Refine', 6);

%set initial condition: state = [m1 p1 m2 p2 m3 p3] 
x0=[0.2 0.1, 0.3 0.1 0.4 0.5]';

%run simulation 
[t,s]=ode45(ODEFUN, [0,Tend], x0, options);

%produce figure 7.21A 
figure(1) 
set(gca,'fontsize',14) 
t=t/0.3485
plot(t,40*s(:,2), 'k',t,40*s(:,4), 'k--', t,40*s(:,6), 'k:','Linewidth', 3) 
axis([0 800 0 7000]) 
ylabel('protein abundance (molecules per cell)')
xlabel('Time (min)') 
legend('Protein 1', 'Protein 2', 'Protein 3')
end

function dS=repressilatorddt(t,s)

global alpha
global alpha0
global n
global beta

m1=s(1);
p1=s(2);
m2=s(3);
p2=s(4);
m3=s(5);
p3=s(6);

m1ddt= alpha0 + alpha/(1+p3^n) - m1;
p1ddt=beta*(m1-p1);
m2ddt= alpha0 + alpha/(1+p1^n) - m2;
p2ddt=beta*(m2-p2);
m3ddt= alpha0 + alpha/(1+p2^n) - m3;
p3ddt=beta*(m3-p3);   

dS =[m1ddt,  p1ddt, m2ddt, p2ddt, m3ddt, p3ddt]';

end

[Dev]

thanks for the reply..i gt d op