% This file works with OCTAVE and is automatically generated with
% the System Biology Format Converter (http://sbfc.sourceforge.net/)
% from an SBML file.
% To run this file with Matlab you must edit the comments providing
% the definition of the ode solver and the signature for the
% xdot function.
%
% The conversion system has the following limitations:
% - You may have to re order some reactions and Assignment Rules definition
% - Delays are not taken into account
% - You should change the lsode parameters (start, end, steps) to get better results
%
%
% Model name = Morris2002_CellCycle_CDK2Cyclin
%
% is http://identifiers.org/biomodels.db/MODEL4821491663
% is http://identifiers.org/biomodels.db/BIOMD0000000150
% isDescribedBy http://identifiers.org/pubmed/11959850
%
function main()
%Initial conditions vector
x0=zeros(4,1);
x0(1) = 0.0;
x0(2) = 4.0E-7;
x0(3) = 1.0E-7;
x0(4) = 0.0;
% Depending on whether you are using Octave or Matlab,
% you should comment / uncomment one of the following blocks.
% This should also be done for the definition of the function f below.
% Start Matlab code
% tspan=[0:0.01:100];
% opts = odeset('AbsTol',1e-3);
% [t,x]=ode23tb(@f,tspan,x0,opts);
% End Matlab code
% Start Octave code
t=linspace(0,100,100);
x=lsode('f',x0,t);
% End Octave code
plot(t,x);
end
% Depending on whether you are using Octave or Matlab,
% you should comment / uncomment one of the following blocks.
% This should also be done for the definition of the function f below.
% Start Matlab code
%function xdot=f(t,x)
% End Matlab code
% Start Octave code
function xdot=f(x,t)
% End Octave code
% Compartment: id = geometry, name = geometry, constant
compartment_geometry=1.0E-12;
% Parameter: id = basal_fluorescence, name = basal_fluorescence
% Warning parameter basal_fluorescence is not constant, it should be controlled by a Rule and/or events
global_par_basal_fluorescence=1.21210648148148;
% Parameter: id = total_fluorescence, name = total_fluorescence
% assignmentRule: variable = total_fluorescence
global_par_total_fluorescence=x(1)*599990*1E6/43200+x(4)*599990*1E6/43200+global_par_basal_fluorescence;
% Reaction: id = Binding % Local Parameter: id = kf, name = kf
reaction_Binding_kf=1.9E7;
% Local Parameter: id = kb, name = kb
reaction_Binding_kb=25.0;
reaction_Binding=reaction_Binding_kf*x(3)*x(2)*compartment_geometry-reaction_Binding_kb*x(1)*compartment_geometry;
% Reaction: id = Activation % Local Parameter: id = kf, name = kf
reaction_Activation_kf=0.813;
% Local Parameter: id = kb, name = kb
reaction_Activation_kb=0.557;
reaction_Activation=reaction_Activation_kf*x(1)*compartment_geometry-reaction_Activation_kb*x(4)*compartment_geometry;
xdot=zeros(4,1);
% Species: id = CDK2cycA, name = CDK2cycA, affected by kineticLaw
xdot(1) = (1/(compartment_geometry))*(( 1.0 * reaction_Binding) + (-1.0 * reaction_Activation));
% Species: id = CyclinA, name = CyclinA, affected by kineticLaw
xdot(2) = (1/(compartment_geometry))*((-1.0 * reaction_Binding));
% Species: id = Cdk2, name = Cdk2, affected by kineticLaw
xdot(3) = (1/(compartment_geometry))*((-1.0 * reaction_Binding));
% Species: id = CDK2cycA_star_, name = CDK2cycA_star_, affected by kineticLaw
xdot(4) = (1/(compartment_geometry))*(( 1.0 * reaction_Activation));
end
% adding few functions representing operators used in SBML but not present directly
% in either matlab or octave.
function z=pow(x,y),z=x^y;end
function z=root(x,y),z=y^(1/x);end
function z = piecewise(varargin)
numArgs = nargin;
result = 0;
foundResult = 0;
for k=1:2: numArgs-1
if varargin{k+1} == 1
result = varargin{k};
foundResult = 1;
break;
end
end
if foundResult == 0
result = varargin{numArgs};
end
z = result;
end