addparameter

Create parameter object and add to model or kinetic law object

Syntax

parameterObj = addparameter(modelKineticLawObj,parameterName)

parameterObj = addparameter(modelKineticLawObj,parameterName,parameterValue)

parameterObj = addparameter(___,Name=Value)

Description

parameterObj = addparameter(modelKineticLawObj,parameterName) creates and returns a Parameter object parameterObj. The function also assigns

• parameterName to the Name property of parameterObj.

• modelKineticLawObj to the Parent property of parameterObj.

• parameterObj to the Parameters property of the model object or kinetic law object modelKineticLawObj.

• A value of 1 to the Value property of parameterObj.

parameterObj = addparameter(modelKineticLawObj,parameterName,parameterValue) also assigns the Value property of parameterObj to parameterValue.

parameterObj = addparameter(___,Name=Value) also sets the properties of the parameter object using one or more name-value arguments. Name is the property name and Value is the corresponding value.

Examples

Add Parameters to SimBiology Model

Create a model and add a reaction.

modelObj = sbiomodel('my_model');
reactionObj = addreaction(modelObj,'a + b -> c + d');

Define a kinetic law for the reaction object.

kineticlawObj = addkineticlaw(reactionObj, 'MassAction');

Add a parameter and assign it to the kinetic law object.

parameterObj1 = addparameter(kineticlawObj,'K1');

Add parameter with value 0.9 to the model object.

parameterObj2 = addparameter(modelObj,'K2',0.9);

Use get to retrieve a list of parameters that are scoped to the kinetic law object and model object.

get(kineticlawObj,'Parameters')

ans = 
   SimBiology Parameter Array

   Index:    Name:    Value:    Units:
   1         K1       1               

get(modelObj,'Parameters')

ans = 
   SimBiology Parameter Array

   Index:    Name:    Value:    Units:
   1         K2       0.9             

Input Arguments

modelKineticLawObj — SimBiology model or kinetic law

SimBiology.Model | SimBiology.KineticLaw

SimBiology model or kinetic law, specified as a Model or SimBiology.KineticLaw object.

parameterName — Name of parameter

character vector | string scalar

Name of the parameter object, specified as a character vector or string scalar.

Data Types: char | string

parameterValue — Value of parameter

1 (default) | numeric scalar

Value of the parameter, specified as a numeric scalar.

Data Types: double

More About

Scope of SimBiology Parameter

A parameter object defines an assignment that a model or a kinetic law can use. The scope of the parameter is defined by the parameter parent.

If a parameter object is defined with a model object as its parent, then all objects within the model (including all rules, events and kinetic laws) can use the parameter. Consider the following.

modelObj = sbiomodel('cell')
parameterObj = addparameter(modelObj, 'TF1', 0.01)

The parameter object is added to the model object, which becomes the parent of parameterObj.

If a parameter is defined with a kinetic law object, then only the kinetic law object and objects within the kinetic law object can use the parameter.

modelObj = sbiomodel('cell')
reactionObj = addreaction(modelObj, 'a -> b')
kineticlawObj = addkineticlaw (reactionObj, 'MassAction')
parameterObj = addparameter(kineticlawObj, 'K1_forward', 0.1)

When a kinetic law searches for a parameter in its expression, it first looks in the parameter list of the kinetic law. If the parameter isn’t found there, it moves to the model that the kinetic law object is in and looks in the model parameter list. If the parameter isn’t found there, it moves to the model parent.

When a rule searches for a parameter in its expression, it looks in the parameter list for the model. If the parameter isn’t found there, it moves to the model parent. A rule cannot use a parameter that is scoped to a kinetic law. So for a parameter to be used in both a reaction rate equation and a rule, the parameter should be scoped to a model.

Version History

Introduced in R2006a

R2024a: Having duplicate model component names is no longer allowed

• When you load a model that contains duplicate names, SimBiology automatically updates those names. SimBiology disambiguates the duplicate names by adding a suffix "_N", where N is the first positive integer that results in a unique name. If there is an existing suffix, N will be incremented from that suffix. For example, if there are two model components named x_3, the function updates one of the names to x_4. If the existing suffix has leading zeros, the function omits the zeros in the new name. For instance, if x_003 is a duplicate name, it gets renamed to x_4. However, the function assumes that names with leading zeros and without leading zeros are different. For instance, x_005 and x_5 are considered to be different names.

• SimBiology issues an error if multiple model components (model, compartment, species, parameter, reaction, rule, event, observable, dose, and variant) have the same name. Within a single model, these components are required to have unique names even when they are of different types with the following two exceptions:

  • Species in different compartments can have the same name.

  • Parameters can have the same name if they are scoped to different parents. Specifically, you can use the same name for a model-scoped parameter and reaction-scoped parameters, where each reaction-scoped parameter belongs to a different reaction.

  For details on how to reference model component names in expressions, see Guidelines for Referencing Names in Expressions.

R2022b: Having duplicate model component names issues a warning

SimBiology issues a warning if multiple model components have the same name.

R2022a: Having duplicate model component names will not be allowed in a future release

SimBiology will not allow you to have duplicate names for model components within a model.