IGEM:Melbourne/2008/BioClock/David Version/run clock code

clear all; close all;

format long e;

delete time_v2.dat delete sg0_v2.dat

global pulse tau_on tau_off

% x0 = bioclock_core_v3; % initial conditions % t_end = 100; error = 1e-6;

% x0(1) = 1; % change sg0 to single pulse ... this can be changed later options = odeset('RelTol',error,'AbsTol',error); % options

% [time_sim x_sim] = ode23s(@bioclock_core_v3,[0,t_end], x0, options);

% figure; % plot(time_sim,x_sim); % hold on;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%% intermitent pulsing x0 = Stephen_clock; % initial conditions again t_end = 100; pulse = 1; tau_on = 2; tau_off = 29;

[time_sim2 x_sim2] = ode23s(@Stephen_clock,[0 t_end], x0, options);

%%% load data files %%%%% pulsing plots time_v2 = load('time_v2.dat'); sg0_v2 = load('sg0_v2.dat');

%%%%%%% PLOTTING TEMPLATE % figure; % plot(Corner1_time,Corner1_c_OPG,'r'); % hold on; % plot(Corner2_time,Corner2_c_OPG,'g'); % plot(Corner3_time,Corner3_c_OPG,'b'); % plot(Corner4_time,Corner4_c_OPG,'k'); % title('Plot of OPG concentration', 'Fontsize', 12); % xlabel('t [days]'); % ylabel('OPG [pM]'); % legend('Corner1','Corner2','Corner3', 'Corner4',1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% figure; plot(time_v2,sg0_v2); hold on; title('Plot of Sg0 pulse','Fontsize',12); xlabel('t'); ylabel('Sg0 pulse'); legend('Sg0',1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% figure; plot(time_sim2,x_sim2(:,4),'g'); hold on; title('Plot of GFP concentration', 'Fontsize', 12); xlabel('t '); ylabel('GFP [M]'); legend('GFP',1); %%%%%%%%%%%%%%%%%%%%%%%%%%% figure; plot(time_sim2,x_sim2(:,7),'r'); hold on; title('Plot of RFP concentration', 'Fontsize', 12); xlabel('t '); ylabel('RFP [M]'); legend('RFP',1); % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% figure; plot(time_sim2,x_sim2(:,6),'b'); hold on; title('Plot of y concentration', 'Fontsize', 12); xlabel('t '); ylabel('y [M]'); legend('y',1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% figure; plot(time_sim2,x_sim2(:,3),'b'); hold on; title('Plot of X concentration', 'Fontsize', 12); xlabel('t '); ylabel('X [M]'); legend('X',1); % figure; plot(time_sim2,x_sim2(:,5),'r'); hold on; title('Plot of Ribokey1 concentration', 'Fontsize', 12); xlabel('t '); ylabel('Ribokey1 [M]'); legend('Ribokey1',1);