ADMITimportModel

ADMITimportModel imports an SBmodel (SBToolbox2) or an SBML model.

OPTOUT = 
  ADMITimportModel(OPT, TIME, MODEL)
OPTOUT = 
  ADMITimportModel(OPT, TIME, MODEL, OPTIONS)  
OPTOUT = 
  ADMITimportModel(OPT, TIME, MODEL, SELECTEDSTATES)  
OPTOUT = 
  ADMITimportModel(OPT, TIME, MODEL, SELECTEDSTATES, OPTIONS)  
 
Reads model from the file named MODEL if MODEL is a string, 
or takes MODEL to be a SBmodel. Adds the model equations to OPT and 
returns the output in OPTOUT.

TIME is a name of a ADMITtime object, or a valid ADMITtime object, for
which the dynamics are considered. If a valid ADMITtime object is
provided, then it is added to the ADMITproject if it isn't present.

If the second input argument SELECTEDSTATES is provided,
then a subSYStem of ODEs, parameters, and variables containing the 
selected states is returned. States which are not selected
but which appear in the ODEs are considered as time-variant inputs and
are returned in the parameter structure (see below).

Inputs
  OPT            : valid ADMITproject
  MODEL          : filename (of SBtoolbox2 or SBML model),
                   or SBmodel/SBmodelBC
  SELECTEDSTATES : cell array of strings with names representing a 
                   subset of states to be selected
  TIME           : string representing a ADMITtime object, 
                   or (named) ADMITtime object; 
                   dynamics are considered for this time point set;
Returns
  OPTOUT         : ADMITproject-object with added model equations

Examples

 To run the following example change to the folder
 ./examples/MichaelisMenten

Import and modification of an SBToolbox2 model

opt = ADMITproject();
% add simulation time 't_sim'
opt = opt + ADMITtime('t_sim := {0:10}')
opt = ADMITimportModel(opt,'t_sim','MichaelisMenten.txt')
% Since no parameter uncertainties are given in the model, we set them
% delete bounds on p1
opt = opt - ADMITconstraint('p1 := [*]');      
% set uncertainties on p1
opt = opt + ADMITconstraint('p1 := [0.1,10]'); 
% you can do the same for p2, p3 etc.
% delete bounds on s(t) and c(t)
opt = opt - ADMITconstraint('s(t_sim) := [*]'); 
opt = opt - ADMITconstraint('c(t_sim) := [*]'); 
% set uncertainties on s(t) and c(t) for all time points (represented by *)
opt = opt + ADMITconstraint('s(*) := [0.0,1]'); 
opt = opt + ADMITconstraint('c(*) := [0.0,1]'); 
% Next we simplify the model and remove some unnecessary variables and
% constants; note: a model with fewer variables might be computationally
% advantageous
% remove (constant) variable e_tot
opt = opt - ADMITvariable('e_tot');
% remove fluxes v_a, v_d, v_t from problem; they are replaced by their
% definition
opt = opt - ADMITvariable('v_a');
opt = opt - ADMITvariable('v_d');
opt = opt - ADMITvariable('v_t');
% last, we remove state e
opt = opt - ADMITvariable('e');
% display result
opt

Import of an SBML model

opt = ADMITproject();
% add simulation time 't_sim'
opt = opt + ADMITtime('t_sim := {0:10}')
opt = ADMITimportModel(opt,'t_sim','MichaelisMenten.xml')
% now you can continue as in example 1)

Select states or subsystem to be imported

opt = ADMITproject();
% add simulation time 't_sim'
opt = opt + ADMITtime('t_sim := {0:10}')
opt = ADMITimportModel(opt,'t_sim','MichaelisMenten.xml',{'c'})
% Note: Only the dynamics for state "c" is added; constraints imposed by 
% dynamics for state "s" are neglected; instead "s" is assumed to be a
% time-variant unknown input