SimFunction object

Function-like interface to execute SimBiology models

Description

The SimFunction object provides an interface that allows you to execute a SimBiology® model like a function and a workflow to perform parameter scans (in parallel if Parallel Computing Toolbox™ is available), Monte Carlo simulations, and scans with multiple or vectorized doses. Since a SimFunction object can be executed like a function handle, you can customize it to integrate SimBiology models with other MATLAB® products and other custom analyses (such as visual predictive checks).

Use the createSimFunction method to construct the SimFunction object. SimFunction objects are immutable once created and automatically accelerated at the first function execution.

Syntax

If you specified any dosing information when you called createSimFunction to construct the SimFunction object F, then F has these signatures.

simdata = F(phi,t_stop,u,t_output) returns a SimData object simdata after simulating a SimBiology model using phi, a matrix of parameter values, t_stop, simulation stop time, u, dosing information, and t_output, output time.

simdata = F(phi,t_stop,u) uses the input arguments phi, t_stop, and u.

If you did not specify any dosing information when you called createSimFunction, then F has these signatures:

simdata = F(phi,t_stop) returns a SimData object simdata using phi and t_stop.

simdata = F(phi,t_stop,[],t_output) uses the input arguments phi, t_stop, empty dosed argument [], and t_output. You must specify u, the dosing information, as an empty array[] for this signature.

    Note:   When t_output is empty and t_stop is specified, the simulations report the solver time points until t_stop. When t_output is specified and t_stop is empty, only the time points in t_output are reported. When both are specified, the reported time points are the union of solver time points and the time points in t_output. If the last t_output is greater than the corresponding t_stop, then simulation proceeds until the last time point in t_output.

simdata = F(phi,tbl) uses the input arguments phi and tbl. Using this signature only lets you specify output times as one of the variables of tbl.

[T,Y] = F(_) returns T, a cell array of numeric vector, and Y, a cell array of 2-D numeric matrices, using any of the input arguments in the preceding syntaxes.

Input Arguments

phi

Matrix of size S-by-P, where S is the number of simulations to perform and P is the number of parameters specified in the params argument when you called createSimFunction to construct F. Each simulation is performed with the parameters specified in the corresponding row of phi.

When phi is specified as a 1-by-P matrix, then all simulations use the same parameters, and the number of simulations is determined from the t_stop, u, or t_output argument in that order.

For example, if phi and t_stop have a single row and u is a matrix of size N-by-DoseTargets, the number of simulations is determined as N.

t_stop

  • Scalar specifying the same stop time for all simulations

  • Vector of size N specifying a stop time for each simulation for all N simulations

u

  • table of dosing information with two or three variables representing dose time, dose amount, and dose rate (optional). You must name the table variables as follows.

    u.Properties.VariableNames = {'Time','Amount','Rate'};

    If UnitConversion is on, specify units for each variable. For instance, you can specify units as follows.

    u.Properties.VariableUnits = {'second','molecule','molecule/second'};

    This table can have multiple rows, where each row represents a dose applied to the dose target at a specified dose time with a specified amount and rate if available.

  • table with one row and five variables containing RepeatDose data. Dose rate variable is optional. Name the variables as follows.

    u.Properties.VariableNames = {'StartTime','Amount','Rate','Interval','RepeatCount'};

    If UnitConversion is on, specify units for each variable. Units for 'RepeatCount' variable can be empty '' or 'dimensionless'. The unit of the 'Amount' variable must be dimensionally consistent with that of the target species. For example, if the unit of target species is in an amount unit (such as mole or molecule), then the 'Amount' variable unit must have the same dimension, i.e., its unit must be an amount unit and cannot be a mass unit (such as gram or kilogram). The unit for the 'Rate' variable must be dimensionally consistent as well.

    u.Properties.VariableUnits = {'second','molecule','molecule/second','second','dimensionless'};
  • Cell array of tables of size 1-by-N, where N is the number of dose targets. Each cell represents a table as described previously.

  • Cell array of tables of size S-by-N, where S is the number of simulations and N is the number of dose targets. Each cell represents a table. S is equal to the number of rows in phi.

t_output

  • Vector of monotonically increasing output times that is applied to all simulations

  • Cell array containing a single time vector that is applied to all simulations

  • Cell array of vectors representing output times. The ith cell element provides the output times for the ith simulation. The number of elements in the cell array must match the number of rows (simulations) in phi.

tbl

table or dataset that has time and dosing information such as group labels, independent variable, dependent variable(s), amount(s), and rate(s). You must name the variables of the table or data set as 'GROUP','TIME','DEPENDENTVAR1','DEPENDENTVAR2',...,'AMOUNT1','RATE1','AMOUNT2','RATE2',.... The rate variable is optional for each dose.

If the dosed argument was empty when creating F, then amount- and rate-related variables are not required. If it is not empty, the number of amount and rate variables must match the number of dosed targets or species in dosed. The number of dependent variables must match the number of columns in phi.

If UnitConversion is on, specify a unit for each variable. The unit of 'Amount' variable must be dimensionally consistent with that of the target species. See the description of the input argument u for details.

Output Arguments

simdata

Array of SimData objects that contains results from executing the SimFunction F. The number of elements in the simdata array is the same as the number of rows in phi. The number of columns in each element of the simdata array, that is, simdata(i).Data, is equal to the number of elements in the observed cell array which was specified when creating F.

T

Cell array containing a numeric vector of size S x 1. S is the number of simulations. The ith element of T contains the time point from the ith simulation.

Y

Cell array of 2-D numeric matrices. The ith element of Y contains data from the ith simulation. The number of rows in T{i} is equal to the number of rows in Y{i}.

Constructor Summary

createSimFunction (model)Create SimFunction object

Method Summary

accelerate(SimFunction)Prepare SimFunction object for accelerated simulations
isaccelerated(SimFunction)Determine if SimFunction object is accelerated

Property Summary

Parameters

table with variables named:

  • 'Name'

  • 'Value'

  • 'Type'

  • 'Units' (only if UnitConversion is turned on)

The table contains information about model quantities (species, compartments, or parameters) that define the inputs of a SimFunction object. For instance, this table can contain parameters or species whose values are being scanned by the SimFunction object. This property is read only.

Observables

table with variables named:

  • 'Name'

  • 'Type'

  • 'Units' (only if UnitConversion is turned on)

This table contains information about model quantities (species, compartments, or parameters) that define the output of a SimFunction object. This property is read only.

Dosed

table containing dosing information with variables named:

  • 'TargetName'

  • 'TargetDimension' (only if UnitConversion is turned on)

  • 'DurationParameterName'

  • 'DurationParameterValue'

  • 'DurationParameterUnits' (only if UnitConversion is turned on)

  • 'LagParameterName'

  • 'LagParameterValue'

  • 'LagParameterUnits' (only if UnitConversion is turned on)

Variables related to the lag and duration parameters are included only when 'LagParameterName' and 'DurationParameterName' are not empty. This property is read only.

UseParallel

Logical. If true and Parallel Computing Toolbox is available, SimFunction is executed in parallel. This property is read-only.

UnitConversion

Logical. If true:

  • During the execution of the SimFunction object, phi is assumed to be in the same units as units for corresponding model quantities specified in the params argument when the object was created using the createSimFunction method.

  • Time (t_output or t_stop) is assumed to be in the same unit as the TimeUnits property of the active configset object of the SimBiology model from which F was created.

  • Variables of dose tables (u) must have units specified by setting u.Properties.VariableUnits to a cell array of appropriate units. The dimension of the dose target such as an amount (molecule, mole, etc.) or mass (gram, kilogram, etc.), is stored on the Dosed property of F.

  • The simulation result is in the same units as those specified on the corresponding quantities in the SimBiology model from which F was created.

This property is read only.
DependentFiles

Cell array of strings containing the names of files that the model depends on. This property is used for deployment. This property is read only.

Examples

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Scan Parameters of the Lotka-Volterra Model

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 dose.

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));

Scan Initial Amounts of a Species from a Radioactive Decay Model

This example shows how to scan initial amounts of a species from a radioactive decay model with the first-order reaction: dzdt=c·x, where x and z are species and c is the forward rate constant.

Load the sample project containing the radiodecay model m1.

sbioloadproject radiodecay;

Create a SimFunction object f to scan initial amounts of species x.

f = createSimFunction(m1,{'x'},{'x','z'},[])
f = 

SimFunction

Parameters:

    Name    Value      Type         Units   
    ____    _____    _________    __________

    'x'     1000     'species'    'molecule'

Observables: 

    Name      Type         Units   
    ____    _________    __________

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

Dosed: None

Define four different initial amounts of species x for scanning. The number of rows indicates the total number of simulations, and each simulation uses the parameter value specified in each row of the vector.

phi = [200; 400; 600; 800];

Run simulations until the stop time is 20 and plot the simulation results.

sbioplot(f(phi, 20))

Simulate a Model and Scan Parameters with Doses

This example shows how to simulate and scan a parameter of a radiodecay model while a species is being dosed.

Load the sample project containing the radiodecay model m1.

sbioloadproject radiodecay;

Create a SimFunction object f specifying parameter Reaction1.c to be scanned and species x as a dosed target.

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

Define a scalar dose of amount 200 molecules given at three time points (5, 10, and 15 seconds).

dosetime = [5 10 15];
dose = [200 200 200];
u = table(dosetime', dose');
u.Properties.VariableNames = {'Time','Amount'};
u.Properties.VariableUnits = {'second','molecule'};

Define the parameter values for Reaction1.c to scan.

phi = [0.1 0.2 0.5]';

Simulate the model for 20 seconds and plot the results.

sbioplot(f(phi,20,u));

You can also specify different dose amounts at different times.

d1 = table(5,100);
d1.Properties.VariableNames = {'Time','Amount'};
d1.Properties.VariableUnits = {'second','molecule'};
d2 = table(10,300);
d2.Properties.VariableNames = {'Time','Amount'};
d2.Properties.VariableUnits = {'second','molecule'};
d3 = table(15,600);
d3.Properties.VariableNames = {'Time','Amount'};
d3.Properties.VariableUnits = {'second','molecule'};

Simulate the model using these doses and plot the results.

sbioplot(f(phi,20,{d1;d2;d3}));

You can also define a cell array of dose tables.

u = cell(3,1);
dosetime = [5 10 15];
dose = [200 200 200];
u{1} = table(dosetime',dose');
u{1}.Properties.VariableNames = {'Time','Amount'};
u{1}.Properties.VariableUnits = {'second','molecule'};
dosetime2 = [2 6 12];
dose2 = [500 500 500];
u{2} = table(dosetime2', dose2');
u{2}.Properties.VariableNames = {'Time','Amount'};
u{2}.Properties.VariableUnits = {'second','molecule'};
dosetime3 = [3 8 18];
dose3 = [100 100 100];
u{3} = table(dosetime3', dose3');
u{3}.Properties.VariableNames = {'Time','Amount'};
u{3}.Properties.VariableUnits = {'second','molecule'};

Simulate the model using the dose tables and plot results.

sbioplot(f(phi,20,u));

References

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

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