#
# 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 = Gardner1998_CellCycle_Goldbeter
#
# is urn:miriam:biomodels.db:BIOMD0000000008
# is urn:miriam:biomodels.db:MODEL6614879888
# isDescribedBy urn:miriam:pubmed:9826676
# isDescribedBy urn:miriam:biomodels.db:BIOMD0000000003
#
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 = Cell, name = Cell, constant
	compartment_Cell=1.0;
# Parameter:   id =  V1, name = V1
# Parameter:   id =  K6, name = K6
	global_par_K6=0.3;
# Parameter:   id =  V1p, name = V1p
	global_par_V1p=0.75;
# Parameter:   id =  V3, name = V3
# Parameter:   id =  V3p, name = V3p
	global_par_V3p=0.3;
# assignmentRule: variable = V1
	global_par_V1=x(1)*global_par_V1p*(x(1)+global_par_K6)^(-1);
# assignmentRule: variable = V3
	global_par_V3=x(3)*global_par_V3p;
# Reaction: id = reaction1, name = creation of cyclin

	# Local Parameter:   id =  vi, name = vi
	reaction_reaction1_vi=0.1;

	reaction_reaction1=reaction_reaction1_vi;
# Reaction: id = reaction2, name = cdc2 kinase triggered degration of cyclin

	# Local Parameter:   id =  k1, name = k1
	reaction_reaction2_k1=0.5;
	# Local Parameter:   id =  K5, name = K5
	reaction_reaction2_K5=0.02;

	reaction_reaction2=x(1)*reaction_reaction2_k1*x(2)*(x(1)+reaction_reaction2_K5)^(-1);
# Reaction: id = reaction3, name = default degradation of cyclin

	# Local Parameter:   id =  kd, name = kd
	reaction_reaction3_kd=0.02;

	reaction_reaction3=x(1)*reaction_reaction3_kd;
# Reaction: id = reaction4, name = activation of cdc2 kinase

	# Local Parameter:   id =  K1, name = K1
	reaction_reaction4_K1=0.1;

	reaction_reaction4=(1- 1*x(3))*global_par_V1*(reaction_reaction4_K1- 1*x(3)+1)^(-1);
# Reaction: id = reaction5, name = deactivation of cdc2 kinase

	# Local Parameter:   id =  V2, name = V2
	reaction_reaction5_V2=0.25;
	# Local Parameter:   id =  K2, name = K2
	reaction_reaction5_K2=0.1;

	reaction_reaction5=x(3)*reaction_reaction5_V2*(reaction_reaction5_K2+x(3))^(-1);
# Reaction: id = reaction6, name = activation of cyclin protease

	# Local Parameter:   id =  K3, name = K3
	reaction_reaction6_K3=0.2;

	reaction_reaction6=global_par_V3*(1- 1*x(2))*(reaction_reaction6_K3- 1*x(2)+1)^(-1);
# Reaction: id = reaction7, name = deactivation of cyclin protease

	# Local Parameter:   id =  K4, name = K4
	reaction_reaction7_K4=0.1;
	# Local Parameter:   id =  V4, name = V4
	reaction_reaction7_V4=0.1;

	reaction_reaction7=reaction_reaction7_V4*x(2)*(reaction_reaction7_K4+x(2))^(-1);
# Reaction: id = reaction8, name = reaction8

	# Local Parameter:   id =  a1, name = a1
	reaction_reaction8_a1=0.05;

	reaction_reaction8=reaction_reaction8_a1*x(1)*x(4);
# Reaction: id = reaction9, name = reaction9

	# Local Parameter:   id =  a2, name = a2
	reaction_reaction9_a2=0.05;

	reaction_reaction9=reaction_reaction9_a2*x(5);
# Reaction: id = reaction10, name = desinhibition of cyclin

	# Local Parameter:   id =  alpha, name = alpha
	reaction_reaction10_alpha=0.1;
	# Local Parameter:   id =  d1, name = d1
	reaction_reaction10_d1=0.05;

	reaction_reaction10=reaction_reaction10_alpha*reaction_reaction10_d1*x(5);
# Reaction: id = reaction11, name = degradation of inhibited cyclin

	# Local Parameter:   id =  kd, name = kd
	reaction_reaction11_kd=0.02;
	# Local Parameter:   id =  alpha, name = alpha
	reaction_reaction11_alpha=0.1;

	reaction_reaction11=reaction_reaction11_alpha*reaction_reaction11_kd*x(5);
# Reaction: id = reaction12, name = creation of cyclin inhibitor

	# Local Parameter:   id =  vs, name = vs
	reaction_reaction12_vs=0.2;

	reaction_reaction12=reaction_reaction12_vs;
# Reaction: id = reaction13, name = degradation of cyclin inhibitor

	# Local Parameter:   id =  d1, name = d1
	reaction_reaction13_d1=0.05;

	reaction_reaction13=reaction_reaction13_d1*x(4);
	xdot=zeros(5,1);
	# Species:   id = C, name = cyclin, affected by kineticLaw

	xdot(1) = (1/(compartment_Cell))*(( 1.0 * reaction_reaction1) + (-1.0 * reaction_reaction2) + (-1.0 * reaction_reaction3) + (-1.0 * reaction_reaction8) + ( 1.0 * reaction_reaction9) + ( 1.0 * reaction_reaction10));

	# Species:   id = X, name = protease, affected by kineticLaw

	xdot(2) = (1/(compartment_Cell))*(( 1.0 * reaction_reaction6) + (-1.0 * reaction_reaction7));

	# Species:   id = M, name = cdc2k, affected by kineticLaw

	xdot(3) = (1/(compartment_Cell))*(( 1.0 * reaction_reaction4) + (-1.0 * reaction_reaction5));

	# Species:   id = Y, name = cyclin inhibitor, affected by kineticLaw

	xdot(4) = (1/(compartment_Cell))*((-1.0 * reaction_reaction8) + ( 1.0 * reaction_reaction9) + ( 1.0 * reaction_reaction11) + ( 1.0 * reaction_reaction12) + (-1.0 * reaction_reaction13));

	# Species:   id = Z, name = complex inhibitor-cyclin, affected by kineticLaw

	xdot(5) = (1/(compartment_Cell))*(( 1.0 * reaction_reaction8) + (-1.0 * reaction_reaction9) + (-1.0 * reaction_reaction10) + (-1.0 * reaction_reaction11));

endfunction

#Initial conditions vector
x0=zeros(5,1);
x0(1) = 0.0;
x0(2) = 0.0;
x0(3) = 0.0;
x0(4) = 1.0;
x0(5) = 1.0;


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

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

#ploting the results
plot(t,x);