% 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 = Kim2011_Oscillator_SimpleIII
%
% is http://identifiers.org/biomodels.db/MODEL1012090001
% is http://identifiers.org/biomodels.db/BIOMD0000000323
% isDescribedBy http://identifiers.org/pubmed/21283141
%


function main()
%Initial conditions vector
	x0=zeros(3,1);
	x0(1) = 0.0;
	x0(2) = 0.0;
	x0(3) = 0.33;


% 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 = compartment_1, name = compartment, constant
	compartment_compartment_1=1.0;
% Parameter:   id =  parameter_1, name = alpha
	global_par_parameter_1=1.0;
% Parameter:   id =  parameter_2, name = beta
	global_par_parameter_2=0.3;
% Parameter:   id =  parameter_3, name = n
	global_par_parameter_3=5.0;

% Reaction: id = reaction_1, name = reaction1	% Local Parameter:   id =  Shalve, name = Shalve
	reaction_reaction_1_Shalve=1.0;

	reaction_reaction_1=compartment_compartment_1*function_1(global_par_parameter_1, reaction_reaction_1_Shalve, global_par_parameter_3, x(1));

% Reaction: id = reaction_2, name = reaction2	% Local Parameter:   id =  Shalve, name = Shalve
	reaction_reaction_2_Shalve=1.0;

	reaction_reaction_2=compartment_compartment_1*function_1(global_par_parameter_1, reaction_reaction_2_Shalve, global_par_parameter_3, x(2));

% Reaction: id = reaction_3, name = reaction3	% Local Parameter:   id =  Shalve, name = Shalve
	reaction_reaction_3_Shalve=1.0;

	reaction_reaction_3=compartment_compartment_1*function_1(global_par_parameter_1, reaction_reaction_3_Shalve, global_par_parameter_3, x(3));

% Reaction: id = reaction_4, name = reaction4
	reaction_reaction_4=compartment_compartment_1*function_3(x(1), global_par_parameter_2);

% Reaction: id = reaction_5, name = reaction5
	reaction_reaction_5=compartment_compartment_1*function_3(x(2), global_par_parameter_2);

% Reaction: id = reaction_6, name = reaction6
	reaction_reaction_6=compartment_compartment_1*function_3(x(3), global_par_parameter_2);

	xdot=zeros(3,1);
	
% Species:   id = species_1, name = x1, affected by kineticLaw
	xdot(1) = (1/(compartment_compartment_1))*((-1.0 * reaction_reaction_1) + ( 1.0 * reaction_reaction_1) + ( 1.0 * reaction_reaction_2) + (-1.0 * reaction_reaction_4));
	
% Species:   id = species_2, name = x2, affected by kineticLaw
	xdot(2) = (1/(compartment_compartment_1))*((-1.0 * reaction_reaction_2) + ( 1.0 * reaction_reaction_2) + ( 1.0 * reaction_reaction_3) + (-1.0 * reaction_reaction_5));
	
% Species:   id = species_3, name = x3, affected by kineticLaw
	xdot(3) = (1/(compartment_compartment_1))*(( 1.0 * reaction_reaction_1) + (-1.0 * reaction_reaction_3) + ( 1.0 * reaction_reaction_3) + (-1.0 * reaction_reaction_6));
end

function z=function_1(V,Shalve,h,substrate), z=(V/(Shalve^h+substrate^h));end

function z=function_3(x,beta), z=(x/beta/(1+x/beta));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


