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getequations

Return system of equations for model object

Syntax

equations = getequations(modelobj)
equations = getequations(modelobj,configsetobj,variantobj,doseobj)

Description

equations = getequations(modelobj) returns equations, a character vector containing the system of equations that represent modelobj, a model object. The active Configset object is used to generate the equations and must specify a deterministic solver.

equations = getequations(modelobj,configsetobj,variantobj,doseobj) returns the system of equations that represent the model specified by a Model object, Variant objects, and dose objects (RepeatDose or ScheduleDose). The Configset object, configsetobj, is used to generate the equations and must specify a deterministic solver.

Tips

Use getequations to see the system of equations that represent a model for:

  • Publishing purposes

  • Model debugging

Input Arguments

modelobj

Object of the Model class.

    Note:   If using modelobj as the only input argument, the active Configset object must specify a deterministic solver.

configsetobj

Object of the Configset class. This object must specify a deterministic solver.

Default: [] (Empty, which specifies the active Configset object for modelobj)

variantobj

Object or array of objects of the Variant class.

Default: [] (Empty, which specifies no variant object)

doseobj

Object or array of objects of the RepeatDose or ScheduleDose class.

Default: [] (Empty, which specifies no dose object)

Output Arguments

equations

Character vector containing the system of equations that represent a model. Equations for reactions, rules, events, variants, and doses are included.

Examples

expand all

View system of equations that represent a simple model, containing only reactions.

Import the lotka model, included with SimBiology®, into a variable named model1:

model1 = sbmlimport('lotka');

View all equations that represent the model1 model and its active configset:

m1equations = getequations(model1)
m1equations =

ODEs:
d(y1)/dt = 1/unnamed*(ReactionFlux1 - ReactionFlux2)
d(y2)/dt = 1/unnamed*(ReactionFlux2 - ReactionFlux3)
d(z)/dt = 1/unnamed*(ReactionFlux3)

Fluxes:
ReactionFlux1 = c1*y1*x
ReactionFlux2 = c2*y1*y2
ReactionFlux3 = c3*y2

Parameter Values:
c1 = 10
c2 = 0.01
c3 = 10
unnamed = 1

Initial Conditions:
x = 1
y1 = 900
y2 = 900
z = 0

MATLAB® displays the ODEs, fluxes, parameter values, and initial conditions for the reactions in model1.

View system of equations that represent a model, containing only reactions, and a repeated dose.

Import the lotka model, included with SimBiology, into a variable named model1:

model1 = sbmlimport('lotka');

Add a repeated dose to the model:

doseObj1 =  adddose(model1,'dose1','repeat');

Set the properties of the dose to administer 3 mg, at a rate of 10 mg/hour, 6 times, at an interval of every 24 hours, to species y1:

doseObj1.Amount = 0.003;
doseObj1.AmountUnits = 'gram';
doseObj1.Rate = 0.010;
doseObj1.RateUnits = 'gram/hour';
doseObj1.Repeat = 6;
doseObj1.Interval = 24;
doseObj1.TimeUnits = 'hour';
doseObj1.TargetName = 'y1';

View all equations that represent the model1 model, its active configset, and the repeated dose:

m1_with_dose_equations = getequations (model1,[],[],doseObj1)
m1_with_dose_equations =

ODEs:
d(y1)/dt = 1/unnamed*(ReactionFlux1 - ReactionFlux2) + dose1
d(y2)/dt = 1/unnamed*(ReactionFlux2 - ReactionFlux3)
d(z)/dt = 1/unnamed*(ReactionFlux3)

Fluxes:
ReactionFlux1 = c1*y1*x
ReactionFlux2 = c2*y1*y2
ReactionFlux3 = c3*y2

Parameter Values:
c1 = 10
c2 = 0.01
c3 = 10
unnamed = 1

Initial Conditions:
y1 = 900
y2 = 900
z = 0
x = 1

Doses:
Variable                      Type                Units               
dose1                         repeatdose          gram    

MATLAB displays the ODEs, fluxes, parameter values, and initial conditions for the reactions and the dose in model1.


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