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Species object

Object containing species information

Description

The SimBiology® species object represents a species, which 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. The name of each species must be unique within the same compartment and the species object cannot have the same name as any observable object in the model.

To add species that participate in reactions, add the reaction to the model. The process of adding the reaction to the model creates a compartment object (unnamed) and the necessary species objects.

Alternatively, create and add a species object to a compartment object, using the addspecies method at the command line.

See Property Summary for links to species property reference pages. Properties define the characteristics of an object. Use the get and set commands to list object properties and change their values at the command line. You can graphically change object properties in the graphical user interface.

Constructor Summary

addspecies (model, compartment)Create species object and add to compartment object within model object

Method Summary

Methods for species objects

copyobjCopy SimBiology object and its children
deleteDelete SimBiology object
displayDisplay summary of SimBiology object
findUsages (species, parameter, compartment)Find out how a species, parameter, or compartment is used in a model
getGet SimBiology object properties
moveMove SimBiology species or parameter object to new parent
renameRename object and update expressions
setSet SimBiology object properties

Property Summary

Properties for species objects

ActiveIndicate object in use during simulation
BoundaryConditionIndicate species boundary condition
Constant Specify variable or constant species amount, parameter value, or compartment capacity
ConstantAmount Specify variable or constant species amount
InitialAmountSpecies initial amount
InitialAmountUnitsSpecies initial amount units
NameSpecify name of object
NotesHTML text describing SimBiology object
ParentIndicate parent object
TagSpecify label for SimBiology object
TypeDisplay SimBiology object type
Units Units for species amount, parameter value, compartment capacity, observable expression
UserDataSpecify data to associate with object
ValueValue of species, compartment, or parameter object
Introduced in R2006b