#
# This file is automatically generated with 
# the System Biology Format Converter (http://sbfc.sourceforge.net/)
# from an SBML file.
#
# 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
#

#
# The following line is there to be sure that Octave think that this file 
# is a script and not function file
#
1;

#
# Model name = Vilar2006_TGFbeta
#
# is urn:miriam:biomodels.db:BIOMD0000000101
# is urn:miriam:biomodels.db:MODEL4023382414
# isDescribedBy urn:miriam:pubmed:16446785
#
function z=pow(x,y),z=x^y;endfunction
function z=root(x,y),z=y^(1/x);endfunction
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;
		endif
	end
	if foundResult == 0
		result = varargin{numArgs};
	endif
z = result;
endfunction

function xdot=f(x,t)
# Compartment: id = PM, name = Plasma membrane, constant
	compartment_PM=1.0;
# Compartment: id = Endosome, name = Endosome, constant
	compartment_Endosome=1.0;
# Parameter:   id =  ka, name = ka
	global_par_ka=1.0;
# Parameter:   id =  ligand, name = ligand
	global_par_ligand=3.0E-5;
# Parameter:   id =  kcd, name = kcd
	global_par_kcd=0.0277777778;
# Parameter:   id =  klid, name = klid
	global_par_klid=0.25;
# Parameter:   id =  ki, name = ki
	global_par_ki=0.3333333333333;
# Parameter:   id =  pRI, name = pRI
	global_par_pRI=8.0;
# Parameter:   id =  kr, name = kr
	global_par_kr=0.0333333333333333;
# Parameter:   id =  alpha, name = alpha
	global_par_alpha=1.0;
# Parameter:   id =  pRII, name = pRII
	global_par_pRII=4.0;
# Reaction: id = v1, name = Ligand receptor complex formation


	reaction_v1=global_par_ka*global_par_ligand*x(1)*x(2);
# Reaction: id = v2, name = Ligand receptor complex constitutive degradation


	reaction_v2=global_par_kcd*x(3);
# Reaction: id = v3, name = Ligand independent complex degradation


	reaction_v3=global_par_klid*x(3);
# Reaction: id = v4, name = Ligand receptor complex internalization


	reaction_v4=global_par_ki*x(3);
# Reaction: id = v5, name = RI synthesis


	reaction_v5=global_par_pRI;
# Reaction: id = v6, name = RI constitutive degradation


	reaction_v6=global_par_kcd*x(1);
# Reaction: id = v7, name = RI internalization


	reaction_v7=global_par_ki*x(1);
# Reaction: id = v8, name = RI recycling


	reaction_v8=global_par_kr*x(5);
# Reaction: id = v9, name = Ligand Receptor complex recycling


	reaction_v9=global_par_kr*x(4);
# Reaction: id = v10, name = RII synthesis


	reaction_v10=global_par_pRII;
# Reaction: id = v11, name = RII constitutive degradation


	reaction_v11=global_par_kcd*x(2);
# Reaction: id = v12, name = RII internalization


	reaction_v12=global_par_ki*x(2);
# Reaction: id = v13, name = RII recycling


	reaction_v13=global_par_kr*x(6);

#Event: id=event_0000001
	event_event_0000001=t >= 2500;

	if(event_event_0000001) 
		global_par_ligand=0.01;
	endif
	xdot=zeros(6,1);
	# Species:   id = RI, name = Receptor 1, affected by kineticLaw

	xdot(1) = (-1.0 * reaction_v1) + ( 1.0 * reaction_v5) + (-1.0 * reaction_v6) + (-1.0 * reaction_v7) + ( 1.0 * reaction_v8) + ( 1.0 * reaction_v9);

	# Species:   id = RII, name = Receptor 2, affected by kineticLaw

	xdot(2) = (-1.0 * reaction_v1) + ( 1.0 * reaction_v9) + ( 1.0 * reaction_v10) + (-1.0 * reaction_v11) + (-1.0 * reaction_v12) + ( 1.0 * reaction_v13);

	# Species:   id = lRIRII, name = ligand receptor complex-plasma membrane, affected by kineticLaw

	xdot(3) = ( 1.0 * reaction_v1) + (-1.0 * reaction_v2) + (-1.0 * reaction_v3) + (-1.0 * reaction_v4);

	# Species:   id = lRIRII_endo, name = ligand receptor complex-endosome, affected by kineticLaw

	xdot(4) = ( 1.0 * reaction_v4) + (-1.0 * reaction_v9);

	# Species:   id = RI_endo, name = Receptor 1-endosome, affected by kineticLaw

	xdot(5) = ( 1.0 * reaction_v7) + (-1.0 * reaction_v8);

	# Species:   id = RII_endo, name = Receptor 2 endosome, affected by kineticLaw

	xdot(6) = ( 1.0 * reaction_v12) + (-1.0 * reaction_v13);

endfunction

#Initial conditions vector
x0=zeros(6,1);
x0(1) = 20.0;
x0(2) = 20.0;
x0(3) = 0.0;
x0(4) = 40.0;
x0(5) = 0.0;
x0(6) = 0.0;


#Creating linespace
t=linspace(0,90,100);

#Solving equations
x=lsode("f",x0,t);

#ploting the results
plot(t,x);