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Table 1 DOTcvpSB typical input data structure for the drug displacement problem.

From: DOTcvpSB, a software toolbox for dynamic optimization in systems biology

% Example of the DOTcvp simple input file for the drug displacement problem
data.name = 'DrugDisplacement'; % name of the problem
data.odes.parameters(1) = {'A = 232'}; % constant parameters before ODE
data.odes.parameters(2) = {'B = 46.4'};  
data.odes.parameters(3) = {'C = 2152.96'};  
data.odes.res(1) = {'((1+0.2*(y(1)+y(2)))^2/(((1+0.2*(y(1)+y(2)))^2+A+B*y(2))*((1+0.2*(y(1)+y(2)))^2+A+B*y(1))-C*y(1)*y(2)))*(((1+0.2*(y(1)+y(2)))^2+A+B*y(1))*(0.02-y(1))+B*y(1)*(u(1)-2*y(2)))'};
data.odes.res(2) = {'((1+0.2*(y(1)+y(2)))^2/(((1+0.2*(y(1)+y(2)))^2+A+B*y(2))*((1+0.2*(y(1)+y(2)))^2+A+B*y(1))-C*y(1)*y(2)))*(((1+0.2*(y(1)+y(2)))^2+A+B*y(2))*(u(1)-2*y(2))+46.4*(0.02-y(1)))'};
data.odes.res(3) = {'1'};  
data.odes.ic = [0.02 0.0 0.0]; % vector of initial conditions
data.odes.tf = 300.0; % final time
data.nlp.RHO = 5; % CVP discretization level
data.nlp.J0 = 'y(3)'; % performance index, min-max(performance index)
data.nlp.u0 = 4.0; % initial guess for control values
data.nlp.lb = 0.0; % lower bounds for control values
data.nlp.ub = 8.0; % upper bounds for control values
data.nlp.solver = 'IPOPT'; % ['FMINCON'|'IPOPT'|'SRES'|'DE'|'ACOMI'|'MISQP'|'MITS']
data.nlp.FreeTime = 'on'; % ['on'|'off'] set 'on' if free time is considered
data.nlp.eq.status = 'on'; % ['on'|'off'] switch on/off of the equality constraints
data.nlp.eq.NEC = 2; % number of active equality constraints
data.nlp.eq.eq(1) = {'y(1)-0.02'}; % first equality constraint
data.nlp.eq.eq(2) = {'y(2)-2.0'}; % second equality constraint
data.nlp.eq.time(1) = data.nlp.RHO; % to indicate that it is an end-point constraint
data.nlp.eq.time(2) = data.nlp.RHO; % to indicate that it is an end-point constraint
data.options.trajectories = size(data.odes.res,2)-1; % how many state trajectories will be displayed
  1. This table shows a typical input file for DOTcvpSB. Many more options can be set, otherwise their values will be taken from defaults (defined in a file).