% 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 = Pfeiffer2001_ATP-ProducingPathways_CooperationCompetition
%
% is http://identifiers.org/biomodels.db/MODEL1105120000
% is http://identifiers.org/biomodels.db/BIOMD0000000337
% isDescribedBy http://identifiers.org/pubmed/11283355
%
function main()
%Initial conditions vector
x0=zeros(3,1);
x0(1) = 0.111111111111111;
x0(2) = 100.0;
x0(3) = 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 = compartment, name = compartment, constant
compartment_compartment=1.0;
% Parameter: id = v, name = v
global_par_v=10.0;
% Parameter: id = d, name = d
global_par_d=1.0;
% Reaction: id = r1, name = resource production
reaction_r1=global_par_v;
% Reaction: id = r2, name = resource consumption and cell growth 1
reaction_r2=x(2)*x(1)/(1+x(1));
% Reaction: id = r3, name = resource consumption and cell growth 2
reaction_r3=x(3)*20*x(1)/(1+x(1));
% Reaction: id = r4, name = cell death 1
reaction_r4=global_par_d*x(2);
% Reaction: id = r5, name = cell death 2
reaction_r5=global_par_d*x(3);
%Event: id=
event_=time >= 15;
if(event_)
x(3)=0.01;
end
xdot=zeros(3,1);
% Species: id = S, name = S, affected by kineticLaw
xdot(1) = (1/(compartment_compartment))*(( 1.0 * reaction_r1) + (-1.0 * reaction_r2) + (-1.0 * reaction_r3));
% Species: id = N1, name = N1, affected by kineticLaw
xdot(2) = (1/(compartment_compartment))*(( 10.0 * reaction_r2) + (-1.0 * reaction_r4));
% Species: id = N2, name = N2, affected by kineticLaw
xdot(3) = (1/(compartment_compartment))*(( 1.0 * reaction_r3) + (-1.0 * reaction_r5));
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