SimBiology^®

sbiospecies - Construct species object

Note sbiospecies produces a warning and will be removed in a future version. Use addspecies instead.

Syntax

speciesObj = sbiospecies('NameValue') speciesObj = sbiospecies('NameValue'),InitialAmountValue) speciesObj = sbiospecies(...'PropertyName', PropertyValue...)

Arguments

NameValue

Name for a species object. Enter a character string unique to the level of object creation. Species objects are identified by Name within ReactionRate and Rule property strings.

You can use the function sbioselect to find an object with a specific Name property value.

For information on naming species see Name.

IntialAmountValue Initial amount value for the species object. Enter double. Positive real number, default = 0.

Description

speciesObj = sbiospecies('NameValue') constructs a SimBiology.Species object, enters a value (NameValue) for the property Name, and returns the object (speciesObj).

speciesObj = sbiospecies('NameValue'),InitialAmountValue) in addition to the above, assigns an initial amount (InitialAmountValue) for the species.

Species are entities that take part in reactions. A species object represents these entities. There are reserved characters you cannot use in species object name (NameValue)

In order for a species object to be used in a simulation, the species object must be added to a SimBiology^® model object using copyobj. You can use addspecies to simultaneously create a species object and add it to a compartment object. A compartment object is constructed with the function addcompartment.

speciesObj = sbiospecies(...'PropertyName', PropertyValue...) defines optional properties. The property name/property value pairs can be in any format supported by the function set (for example, name-value string pairs, structures, and name-value cell array pairs).

View species object properties with the function get, and change properties with the function set. You can find help for speciesObj properties with the help PropertyName command and help for functions with the sbiohelp FunctionName command.

A species is a chemical or entity that participates in reactions, for example, DNA, ATP, Pi, creatine , G-Protein, or Mitogen-Activated Protein Kinase (MAPK). Species amounts can vary or remain constant during a simulation.

If you change the Name property of a species you must configure all applicable elements, such as rules that use the species, any user-specified ReactionRate, or the kinetic law object property SpeciesVariableNames. Use the method setspecies to configure SpeciesVariableNames.

To update species names in the SimBiology graphical user interface, access each appropriate pane through the Project Explorer. You can also use the Find feature to locate the names that you want to update. The Output pane opens with the results of Find. Double-click a result row to go to the location of the model component.

Species names are automatically updated for reactions that use MassAction kinetic law. See Name for more information about specifying species names.

Method Summary

Methods for species objects.

copyobj (any object)	Copy SimBiology^® object and its children
delete (any object)	Delete SimBiology^® object
display (any object)	Display summary of SimBiology^® object

Property Summary

Properties for species object

Annotation	Store link to URL or file
BoundaryCondition	Indicate species boundary condition
ConstantAmount	Specify variable or constant species amount
InitialAmount	Species initial amount
InitialAmountUnits	Species initial amount units
Name	Specify name of object
Notes	HTML text describing SimBiology^® object
Parent	Indicate parent object
Tag	Specify label for SimBiology^® object
Type	Display top-level SimBiology^® object type
UserData	Specify data to associate with object

Examples

Example 1

Create a species (H2O) and view properties for the object.

Create a species object with name H2O and initial amount 1000.

speciesObj = sbiospecies('H2O', 1000);
% View the help for the species object's InitialAmount property.
help(speciesObj, 'InitialAmount')

View properties for the species object.

 get(speciesObj)
            Annotation: ''
     BoundaryCondition: 0
        ConstantAmount: 0
         InitialAmount: 1000
    InitialAmountUnits: ''
                  Name: 'H2O'
                 Notes: ''
                Parent: []
                   Tag: ''
                  Type: 'species'
              UserData: []

Example 2

Create two species, one is a reactant and the other is the enzyme catalyzing the reaction.

Create two species objects with the names glucose_6_phosphate and glucose_6_phosphate_dehydrogenase.

speciesObj1 = sbiospecies ('glucose_6_phosphate');
speciesObj2 = sbiospecies ('glucose_6_phosphate_dehydrogenase');

Set initial amount of glucose_6_phosphate to 100 and verify.

set(speciesObj1, 'InitialAmount', 100);
get(speciesObj1, 'InitialAmount')

MATLAB returns

ans =

   100