% 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 = Lebeda2008 - BoNT paralysis (3 step model)
%
% is http://identifiers.org/biomodels.db/MODEL1009070000
% is http://identifiers.org/biomodels.db/BIOMD0000000267
% isDescribedBy http://identifiers.org/pubmed/18551355
% isDerivedFrom http://identifiers.org/pubmed/6243359
%
function main()
%Initial conditions vector
x0=zeros(4,1);
x0(1) = 1.0;
x0(2) = 0.0;
x0(3) = 0.0;
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 = extracellular, name = extracellular, constant
compartment_extracellular=1.0;
% Compartment: id = endosome, name = endosome, constant
compartment_endosome=1.0;
% Compartment: id = neuroplasm, name = neuroplasm, constant
compartment_neuroplasm=1.0;
% Parameter: id = tension, name = tension
% assignmentRule: variable = tension
global_par_tension=1-x(4);
% Reaction: id = endocytosis % Local Parameter: id = kT, name = kT
reaction_endocytosis_kT=0.141;
reaction_endocytosis=reaction_endocytosis_kT*x(2)*compartment_extracellular;
% Reaction: id = translocation % Local Parameter: id = kL, name = kL
reaction_translocation_kL=0.013;
reaction_translocation=reaction_translocation_kL*x(3)*compartment_endosome;
% Reaction: id = binding % Local Parameter: id = kB, name = kB
reaction_binding_kB=0.058;
reaction_binding=reaction_binding_kB*x(1)*compartment_extracellular;
xdot=zeros(4,1);
% Species: id = free, name = free_BoNT/A, affected by kineticLaw
xdot(1) = (1/(compartment_extracellular))*((-1.0 * reaction_binding));
% Species: id = bound, name = bound_BoNT/A, affected by kineticLaw
xdot(2) = (1/(compartment_extracellular))*((-1.0 * reaction_endocytosis) + ( 1.0 * reaction_binding));
% Species: id = translocate, name = transloc_BoNT/A, affected by kineticLaw
xdot(3) = (1/(compartment_endosome))*(( 1.0 * reaction_endocytosis) + (-1.0 * reaction_translocation));
% Species: id = lytic, name = lytic_BoNT/A, affected by kineticLaw
xdot(4) = (1/(compartment_neuroplasm))*(( 1.0 * reaction_translocation));
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