SimBiology®

Name - Specify name of object

Description

The Nameproperty identifies a SimBiology object. Compartments, species, parameters, 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 non-unique species names if the species are in different compartments, and non-unique parameter names if the parameters are in different kinetic laws or at different levels. Note that having non-unique parameter names can cause the model to have shadowed parameters and that may not be best modeling practice. For more information on levels of parameters see Definition of Parameter Scope in the SimBiology User's Guide.

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 :

• Models names cannot be empty.

• Parameters names cannot be empty, or have the name time.

• 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 square brackets . For example, enclose [DNA polymerase+] within 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+].

• Species and compartments names cannot be empty and note the following reserved words, characters and constraints:

  • The literal words null and time. Note that you can specify species names with these words contained within the name. For example nullaminoacids, or nullnucleotides.

  • The characters ->, <—>,[, and].

For more information on valid MATLAB variable names see genvarname and isvarname.

Characteristics

Example

1. Create a model object with the name my_model.

   modelObj = sbiomodel ('my_model');

2. Add a reaction object to the model object. Note the use of square 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 reaction Name and verify

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

   MATLAB returns

   ans =
   
     Aspartate kinase reaction

See Also

Functions — sbiomodel, sbiounit, sbiounitprefix

Methods — addcompartment, addkineticlaw, addmodel, addparameter, addreaction, addrule, addspecies

Multiplier

Normalization