Name

Specify name of object

Description

The Name property identifies a SimBiology^® object. Compartments, species, parameters, observables, and model objects can be referenced by other objects using the Name property, therefore Name must be unique for these objects. However, species names need only be unique within each compartment. Parameter names must be unique within a model (if at the model level), or within each kinetic law (if at the kinetic law level). This means that you can have nonunique species names if the species are in different compartments, and nonunique parameter names if the parameters are in different kinetic laws or at different levels. Note that having nonunique parameter names can cause the model to have shadowed parameters and that may not be best modeling practice.

Use the function sbioselect to find an object with the same Name property value.

In addition, note the following constraints and reserved characters for the Name property in objects:

• Model and parameter names cannot be empty, the word time, all whitespace, or contain the characters [ or ].

• Compartment and species names cannot be empty, the word null, the word time or contain the characters ->, <->, [ or ].

  • However, compartment and species names can contain the words null and time within the name, such as nulldrug or nullreceptor.

• Reaction, event, and rule names cannot be the word time or contain the characters [ or ].

• If you have a parameter, a species, or compartment name that is not a valid MATLAB^® variable name, when you write an event function, an event trigger, a reaction, reaction rate equation, or a rule you must enclose that name in brackets. For example, enclose [DNA polymerase+] in brackets. In addition, if you have the same species in multiple compartments you must qualify the species with the compartment name, for example, nucleus.[DNA polymerase+], [nuclear complex].[DNA polymerase+].

For more information on valid MATLAB variable names, see matlab.lang.makeValidName, matlab.lang.makeUniqueStrings, and isvarname.

Characteristics

Applies to	Objects: abstract kinetic law, configuration set, compartment, event, kinetic law, model, observable, parameter, reaction, RepeatDose, rule, ScheduleDose, species, unit, or variant
Data type	Character vector
Data values	Any character vector except reserved words and characters
Access	Read/write

Examples

1. Create a model object named my_model.

   modelObj = sbiomodel ('my_model');

2. Add a reaction object to the model object. Note the use of brackets because the names are not valid MATLAB variable names.

   reactionObj = addreaction(modelObj, '[Aspartic acid] -> [beta-Aspartyl-PO4]')

   MATLAB returns:

   SimBiology Reaction Array
   
   Index:    Reaction:
     1       [Aspartic acid] -> [beta-Aspartyl-PO4]

3. Set the reaction Name and verify.

   set (reactionObj, 'Name', 'Aspartate kinase reaction');
   get (reactionObj, 'Name')

   MATLAB returns:

   ans =
   
     Aspartate kinase reaction

Version History

R2022b: Having duplicate model component names issues a warning

• SimBiology issues a warning if multiple model components (model, compartment, species, parameter, reaction, rule, event, observable, dose, and variant) have the same name. In a future release, within a single model, these components will be 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.

  The purpose of this naming restriction is to ensure that every model component can be unambiguously referenced by its unique name within a model. For details on how to reference model component names in expressions, see Guidelines for Referencing Names in Expressions.

• To disambiguate duplicate names from your model, use the updateDuplicateNames function at the command line. The function takes in a SimBiology model as an input and updates the component names as necessary. You can also specify optional outputs, such as a logical flag to check whether any update occurred, a list of model changes, and a copy of the original model before any updates were made.

• The updateDuplicateNames function 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.

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.