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

copyobj	Copy SimBiology object and its children
delete	Delete SimBiology object
display	Display summary of SimBiology object
findUsages	Find out how a species, parameter, or compartment is used in a model
get	Get SimBiology object properties
move	Move SimBiology species or parameter object to new parent
rename	Rename object and update expressions
set	Set SimBiology object properties

Property Summary

Properties for species objects

Active	Indicate object in use during simulation
BoundaryCondition	Indicate species boundary condition
Constant	Specify variable or constant species amount, parameter value, or compartment capacity
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 SimBiology object type
Units	Units for species amount, parameter value, compartment capacity, observable expression
UserData	Specify data to associate with object
Value	Value of species, compartment, or parameter object