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createSimFunction (model)

Create SimFunction object

Syntax

F = createSimFunction(model,params,observables,dosed)
F = createSimFunction(model,params,observables,dosed, variants)
F = createSimFunction(___,Name,Value)

Description

example

F = createSimFunction(model,params,observables,dosed) creates a SimFunction object F that you can execute like a function handle. The params and observables arguments define the inputs and outputs of the function F when it is executed, and dosed defines the dosing information of species. See SimFunction object for details on how to execute F.

example

F = createSimFunction(model,params,observables,dosed, variants) creates a SimFunction object, applying the values stored in variants, a vector of variant objects, as the model baseline values.

example

F = createSimFunction(___,Name,Value) uses additional options specified by one or more Name,Value pair arguments.

    Note:  

    • Active doses and variants of the model are ignored when F is executed.

    • F is immutable after it is created.

    • F is automatically accelerated at the first function execution. However, manually accelerate the object if you want it accelerated in your deployment applications.

Input Arguments

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SimBiology model, specified as a SimBiology model object.

Inputs of SimFunction F, specified as a character vector, cell array of character vectors, or an empty cell array {}. The character vectors represent the names of model quantities (species, compartments, or parameters) that define the inputs of F. Use an empty cell array {} to create a SimFunction object that has no parameters.

To unambiguously name a model quantity, use the qualified name, which includes the name of the compartment. To name a reaction-scoped parameter, use the reaction name to qualify the parameter. If the name is not a valid MATLAB® variable name, surround it by square brackets such as [reaction 1].[parameter 1].

Outputs of SimFunction F, specified as a character vector or cell array of character vectors. The character vectors represent the names of model quantities (species, compartments, or parameters) that define the outputs of F.

Dosed species or dose objects, specified as a character vector, cell array of character vectors, vector of dose objects, or empty array []. If it is a vector, it must be 1-by-N vector, where N is the number of dosed species. Use [] to specify no species are dosed.

If dose objects contain any data for Time, Value, or Rate properties, they are ignored and a warning is issued. Only TargetName, DurationParameterName, and LagParameterName properties of each dose object are used.

Alternate model values, specified as a variant or vector of variant objects. These values are applied as the model baseline values when the SimFunction object is created. If there are multiple variants referring to the same model element, the last occurrence is used.

Name-Value Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside single quotes (' '). You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

Example: 'UseParallel',true specifies to execute the SimFunction F in parallel.

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Flag to execute SimFunction F in parallel, specified as the comma-separated pair consisting of 'UseParallel' and true or false. If true and Parallel Computing Toolbox™ is available, the SimFunction F is executed in parallel.

Example: 'UseParallel',true

Sensitivity output factors, specified as the comma-separated pair consisting of 'SensitivityOutputs' and a cell array of character vectors. The character vectors are the names of model quantities (species and parameters) for which you want to compute the sensitivities. The default is {} meaning there is no output factors. Output factors are the numerators of time-dependent derivatives explained in Sensitivity Calculation.

Use the keyword 'all' to specify all model quantities listed in the observables argument as sensitivity outputs. However, {'all'} means a model quantity named all in the model.

You must specify both 'SensitivityOutputs' and 'SensitivityInputs' name-value pair arguments for sensitivity calculations.

Example: 'SensitivityOutputs','all'

Sensitivity input factors, specified as the comma-separated pair consisting of 'SensitivityInputs' and a cell array of character vectors. The character vectors are the names of model quantities (species, compartments, and parameters) with respect to which you want to compute the sensitivities. The default is {} meaning no input factors. Input factors are the denominators of time-dependent derivatives explained in Sensitivity Calculation.

Use the keyword 'all' to specify all model quantities listed in the params argument as sensitivity inputs. However, {'all'} means a model quantity named all in the model.

You must specify both 'SensitivityOutputs' and 'SensitivityInputs' name-value pair arguments for sensitivity calculations.

Example: 'SensitivityInputs',{'Reaction1.c1','Reaction1.c2'}

Normalization for calculated sensitivities, specified as the comma-separated pair consisting of 'SensitivityNormalization' and 'None', 'Half', or 'Full'.

  • 'None' — No normalization (default)

  • 'Half' — Normalization relative to the numerator only

  • 'Full' — Full dedimensionalization

For details, see Normalization.

Example: 'SensitivityNormalization','Full'

Output Arguments

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SimFunction, returned as a SimFunction object or SimFunctionSensitivity object. You can execute F like a function handle.

F is a SimFunctionSensitivity object if you specify non-empty 'SensitivityOutputs' and 'SensitivityInputs' name-value pair arguments.

Examples

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This example uses a radioactive decay model with the first-order reaction ${{dz} \over {dt}} = c \cdot x$, where x and z are species and c is the forward rate constant.

Load the sample project containing the radioactive decay model m1.

sbioloadproject radiodecay;

Create a SimFunction object, specifying the parameter Reaction1.c to be scanned, and species x as the output of the function with no dosed species.

f = createSimFunction(m1, 'Reaction1.c','x', [])
f = 

SimFunction

Parameters:

        Name         Value       Type          Units   
    _____________    _____    ___________    __________

    'Reaction1.c'    0.5      'parameter'    '1/second'

Observables: 

    Name      Type         Units   
    ____    _________    __________

    'x'     'species'    'molecule'

Dosed: None

If the UnitConversion option was set to false when the SimFunction object f was created, the table does not display the units of the model quantities.

To illustrate this, first set the UnitConversion option to false.

cs = getconfigset(m1);
cs.CompileOptions.UnitConversion = false;

Create the SimFunction object as before and note that the variable named Units disappears.

f = createSimFunction(m1, {'Reaction1.c'},{'x'}, [])
f = 

SimFunction

Parameters:

        Name         Value       Type    
    _____________    _____    ___________

    'Reaction1.c'    0.5      'parameter'

Observables: 

    Name      Type   
    ____    _________

    'x'     'species'

Dosed: None

If any of the species in the model is being dosed, specify the names of dosed species as the last argument. For example, if the species x is being dosed, specify it as the last argument.

f = createSimFunction(m1, {'Reaction1.c'},{'x'}, 'x')
f = 

SimFunction

Parameters:

        Name         Value       Type    
    _____________    _____    ___________

    'Reaction1.c'    0.5      'parameter'

Observables: 

    Name      Type   
    ____    _________

    'x'     'species'

Dosed: 

    TargetName
    __________

    'x'       

Once the SimFunction object is created, you can execute it like a function handle and perform parameter scans (in parallel if Parallel Computing Toolbox™ is available), Monte Carlo simulations, and scans with multiple or vectorized doses. See SimFunction object for more examples.

This example creates a SimFunction object with dosing information using a RepeatDose or ScheduleDose object or a vector of these objects. However, if any dose object contains data such as StartTime, Amount, and Rate, such data are ignored, and a warning is issued. Only data, if available, used are TargetName, LagParameterName, and DurationParameterName of the dose object.

Load the sample project containing the radioactive decay model m1.

sbioloadproject radiodecay;

Create a RepeatDose object and specify its properties.

rdose = sbiodose('rd');
rdose.TargetName = 'x';
rdose.StartTime = 5;
rdose.TimeUnits = 'second';
rdose.Amount = 300;
rdose.AmountUnits = 'molecule';
rdose.Rate = 1;
rdose.RateUnits = 'molecule/second';
rdose.Interval = 100;
rdose.RepeatCount = 2;

Add a lag parameter and duration parameter to the model.

lagPara = addparameter(m1,'lp');
lagPara.Value = 1;
lagPara.ValueUnits = 'second';
duraPara = addparameter(m1,'dp');
duraPara.Value = 1;
duraPara.ValueUnits = 'second';

Set these parameters to the dose object.

rdose.LagParameterName = 'lp';
rdose.DurationParameterName = 'dp';

Create a SimFunction object f using the RepeatDose object rdose that you just created.

f = createSimFunction(m1,{'Reaction1.c'},{'x','z'},rdose)
Warning: Some Dose objects in DOSED had data. This data
will be ignored. 
> In SimFunction>SimFunction.SimFunction at 847
  In SimFunction>SimFunction.createSimFunction at 374 

f = 

SimFunction

Parameters:

        Name         Value       Type          Units   
    _____________    _____    ___________    __________

    'Reaction1.c'    0.5      'parameter'    '1/second'

Observables: 

    Name      Type         Units   
    ____    _________    __________

    'x'     'species'    'molecule'
    'z'     'species'    'molecule'

Dosed: 

    TargetName            TargetDimension        
    __________    _______________________________

    'x'           'Amount(e.g. mole or molecule)'


    DurationParameterName    DurationParameterValue
    _____________________    ______________________

    'dp'                     1                     


    DurationParameterUnits    LagParameterName
    ______________________    ________________

    'second'                  'lp'            


    LagParameterValue    LagParameterUnits
    _________________    _________________

    1                    'second'         

A warning message appears because the rdose object contains data (StartTime, Amount, Rate) that are ignored by the createSimFunction method.

This example shows how to execute different signatures of the SimFunction object to simulate and scan parameters of the Lotka-Volterra (predator-prey) model described by Gillespie [1].

Load the sample project containing the model m1.

sbioloadproject lotka;

Create a SimFunction object f with c1 and c2 as input parameters to be scanned, and y1 and y2 as the output of the function with no dosed species.

f = createSimFunction(m1,{'Reaction1.c1', 'Reaction2.c2'},{'y1', 'y2'}, [])
f = 

SimFunction

Parameters:

         Name         Value       Type    
    ______________    _____    ___________

    'Reaction1.c1'      10     'parameter'
    'Reaction2.c2'    0.01     'parameter'

Observables: 

    Name      Type   
    ____    _________

    'y1'    'species'
    'y2'    'species'

Dosed: None

Define an input matrix that contains values for each parameter (c1 and c2) for each simulation. The number of rows indicates the total number of simulations, and each simulation uses the parameter values specified in each row.

phi = [10 0.01; 10 0.02];

Run simulations until the stop time is 5 and plot the simulation results.

sbioplot(f(phi, 5));

You can also specify a vector of different stop times for each simulation.

t_stop = [3;6];
sbioplot(f(phi, t_stop));

Next, specify the output times as a vector.

t_output = 0:0.1:5;
sbioplot(f(phi,[],[],t_output));

Specify output times as a cell array of vectors.

t_output = {0:0.01:3, 0:0.2:6};
sbioplot(f(phi, [], [], t_output));

This example shows how to calculate sensitivities of some species in the Lotka-Volterra model using the SimFunctionSensitivity object.

Load the sample project.

sbioloadproject lotka;

Define the input parameters.

params = {'Reaction1.c1', 'Reaction2.c2'};

Define the observed species, which are the outputs of simulation.

observables  = {'y1', 'y2'};

Create a SimFunctionSensitivity object. Set the sensitivity output factors to all species (y1 and y2) specified in the observables argument and input factors to those in the params argument (c1 and c2) by using the keyword 'all'.

f = createSimFunction(m1,params,observables,[],'SensitivityOutputs','all','SensitivityInputs','all','SensitivityNormalization','Full')
f = 

SimFunction

Parameters:

         Name         Value       Type    
    ______________    _____    ___________

    'Reaction1.c1'      10     'parameter'
    'Reaction2.c2'    0.01     'parameter'

Observables: 

    Name      Type   
    ____    _________

    'y1'    'species'
    'y2'    'species'

Dosed: None

Sensitivity Input Factors: 

         Name            Type    
    ______________    ___________

    'Reaction1.c1'    'parameter'
    'Reaction2.c2'    'parameter'

Sensitivity Output Factors: 

    Name      Type   
    ____    _________

    'y1'    'species'
    'y2'    'species'

Sensitivity Normalization: 

Full

Calculate sensitivities by executing the object with c1 and c2 set to 10 and 0.1 respectively. Set the output times from 1 to 10. t contains time points, y contains simulation data, and sensMatrix is the sensitivity matrix containing sensitivities of y1 and y2 with respect to c1 and c2.

[t,y,sensMatrix] = f([10,0.1],[],[],1:10);

Retrieve the sensitivity information at simulation time = 5.

temp = sensMatrix{:};
sensMatrix2 = temp(t{:}==5,:,:);
sensMatrix2 = squeeze(sensMatrix2)
sensMatrix2 =

   35.5735   -5.8617
  -39.7255    5.7080

The rows of sensMatrix2 represent output factors (y1 and y2). The columns represent the input factors (c1 and c2).

$$sensMatrix2 = \left[ {\begin{array}{*{20}{c}}
{\begin{array}{*{20}{c}} {\frac{{\partial y1}}{{\partial c1}}}\\ {}\\
{\frac{{\partial y2}}{{\partial c1}}}
\end{array}}&{\begin{array}{*{20}{c}} {\frac{{\partial y1}}{{\partial
c2}}}\\ {}\\ {\frac{{\partial y2}}{{\partial c2}}} \end{array}}
\end{array}} \right]$$

Set the stop time to 15, without specifying the output times. In this case, the output times are the solver time points by default.

sd = f([10,0.1],15);

Retrieve the calculated sensitivities from the SimData object sd.

[t,y,outputs,inputs] = getsensmatrix(sd);

Plot the sensitivities of species y1 and y2 with respect to c1.

figure;
plot(t,y(:,:,1));
legend(outputs);
title('Sensitivites of species y1 and y2 with respect to parameter c1');
xlabel('Time');
ylabel('Sensitivity');

Plot the sensitivities of species y1 and y2 with respect to c2.

figure;
plot(t,y(:,:,2));
legend(outputs);
title('Sensitivites of species y1 and y2 with respect to parameter c2');
xlabel('Time');
ylabel('Sensitivity');

Alternatively, you can use sbioplot. Expand Run1 to select which simulation or sensitivity data to display.

sbioplot(sd);

You can also plot the sensitivity matrix using the time integral for the calculated sensitivities of y1 and y2. The plot indicates y1 and y2 are more sensitive to the parameter c1 than c2.

[~, in, out] = size(y);
result = zeros(in, out);
for i = 1:in
    for j = 1:out
        result(i,j) = trapz(t(:),abs(y(:,i,j)));
    end
end
figure;
hbar = bar(result);
haxes = hbar(1).Parent;
haxes.XTick = 1:length(outputs);
haxes.XTickLabel = outputs;
legend(inputs,'Location','NorthEastOutside');
ylabel('Sensitivity');

This example shows how to simulate the glucose-insulin responses for the normal and diabetic subjects.

Load the model of glucose-insulin response. For details about the model, see the Background section in Simulating the Glucose-Insulin Response.

sbioloadproject('insulindemo', 'm1')

The model contains different initial conditions stored in various variants.

variants = getvariant(m1);

Get the initial conditions for the type 2 diabetic patient.

type2 = variants(1)

   SimBiology Variant - Type 2 diabetic (inactive)

   ContentIndex:     Type:        Name:             Property:           Value:
   1                 parameter    Plasma Volume ... Value               1.49
   2                 parameter    k1                Value               0.042
   3                 parameter    k2                Value               0.071
   4                 parameter    Plasma Volume ... Value               0.04
   5                 parameter    m1                Value               0.379
   6                 parameter    m2                Value               0.673
   7                 parameter    m4                Value               0.269
   8                 parameter    m5                Value               0.0526
   9                 parameter    m6                Value               0.8118
   10                parameter    Hepatic Extrac... Value               0.6
   11                parameter    kmax              Value               0.0465
   12                parameter    kmin              Value               0.0076
   13                parameter    kabs              Value               0.023
   14                parameter    kgri              Value               0.0465
   15                parameter    f                 Value               0.9
   16                parameter    a                 Value               6e-05
   17                parameter    b                 Value               0.68
   18                parameter    c                 Value               0.00023
   19                parameter    d                 Value               0.09
   20                parameter    Stomach Glu Af... Value               125
   21                parameter    kp1               Value               3.09
   22                parameter    kp2               Value               0.0007
   23                parameter    kp3               Value               0.005
   24                parameter    kp4               Value               0.0786
   25                parameter    ki                Value               0.0066
   26                parameter    [Ins Ind Glu U... Value               1
   27                parameter    Vm0               Value               4.65
   28                parameter    Vmx               Value               0.034
   29                parameter    Km                Value               466.21
   30                parameter    p2U               Value               0.084
   31                parameter    K                 Value               0.99
   32                parameter    alpha             Value               0.013
   33                parameter    beta              Value               0.05
   34                parameter    gamma             Value               0.5
   35                parameter    ke1               Value               0.0007
   36                parameter    ke2               Value               269
   37                parameter    Basal Plasma G... Value               164.18
   38                parameter    Basal Plasma I... Value               54.81

Suppress an informational warning that is issued during simulations.

warnSettings = warning('off','SimBiology:DimAnalysisNotDone_MatlabFcn_Dimensionless');

Create SimFunction objects to simulate the glucose-insulin response for the normal and diabetic subjects.

  • Specify an empty array {} for the second input argument to denote that the model will be simulated using the base parameter values (that is, no parameter scanning will be performed).

  • Specify the plasma glucose and insulin concentrations as responses (outputs of the function to be plotted).

  • Specify the species Dose as the dosed species. This species represents the initial concentration of glucose at the start of the simulation.

normSim = createSimFunction(m1,{},...
             {'[Plasma Glu Conc]','[Plasma Ins Conc]'},'Dose')

normSim = 

SimFunction

Parameters:

Observables: 

           Name              Type               Units        
    ___________________    _________    _____________________

    '[Plasma Glu Conc]'    'species'    'milligram/deciliter'
    '[Plasma Ins Conc]'    'species'    'picomole/liter'     

Dosed: 

    TargetName      TargetDimension  
    __________    ___________________

    'Dose'        'Mass (e.g., gram)'

For the diabetic patient, specify the initial conditions using the variant type2.

diabSim = createSimFunction(m1,{},...
             {'[Plasma Glu Conc]','[Plasma Ins Conc]'},'Dose',type2)

diabSim = 

SimFunction

Parameters:

Observables: 

           Name              Type               Units        
    ___________________    _________    _____________________

    '[Plasma Glu Conc]'    'species'    'milligram/deciliter'
    '[Plasma Ins Conc]'    'species'    'picomole/liter'     

Dosed: 

    TargetName      TargetDimension  
    __________    ___________________

    'Dose'        'Mass (e.g., gram)'

Select a dose that represents a single meal of 78 grams of glucose at the start of the simulation.

singleMeal = sbioselect(m1,'Name','Single Meal');

Convert the dosing information to the table format.

mealTable  = getTable(singleMeal);

Simulate the glucose-insulin response for a normal subject for 24 hours.

sbioplot(normSim([],24,mealTable));

Simulate the glucose-insulin response for a diabetic subject for 24 hours.

sbioplot(diabSim([],24,mealTable));

Perform a scan using variants

Suppose you want to perform a parameter scan using an array of variants that contain different initial conditions for different insulin impairments. For example, the model m1 has variants that correspond to the low insulin sensitivity and high insulin sensitivity. You can simulate the model for both conditions via a single call to the SimFunction object.

Select the variants to scan.

varToScan = sbioselect(m1,'Name',...
                    {'Low insulin sensitivity','High insulin sensitivity'});

Check which model parameters are being stored in each variant.

varToScan(1)
   SimBiology Variant - Low insulin sensitivity (inactive)

   ContentIndex:     Type:        Name:             Property:           Value:
   1                 parameter    Vmx               Value               0.0235
   2                 parameter    kp3               Value               0.0045

varToScan(2)
   SimBiology Variant - High insulin sensitivity (inactive)

   ContentIndex:     Type:        Name:             Property:           Value:
   1                 parameter    Vmx               Value               0.094
   2                 parameter    kp3               Value               0.018

Both variants store alternate values for Vmx and kp3 parameters. You need to specify them as input parameters when you create a SimFunction object.

Create a SimFunction object to scan the variants.

variantScan = createSimFunction(m1,{'Vmx','kp3'},...
          {'[Plasma Glu Conc]','[Plasma Ins Conc]'},'Dose');

Simulate the model and plot the results. Run 1 include simulation results for the low insulin sensitivity and Run 2 for the high insulin sensitivity.

sbioplot(variantScan(varToScan,24,mealTable));

Low insulin sensitivity lead to increased and prolonged plasma glucose concentration.

Restore warning settings.

warning(warnSettings);

References

[1] Gillespie, D.T. (1977). Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry. 81(25), 2340–2361.

Introduced in R2014a

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