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Species object

Options for compartment species


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.

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.

When you use the SimBiology desktop to create a new model, it adds an empty compartment (unnamed), to which you can add species.

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 (any object)Copy SimBiology object and its children
delete (any object)Delete SimBiology object
display (any object)Display summary of SimBiology object
findUsages (species, parameter, compartment)Find out how a species, parameter, or compartment is used in a model
get (any object)Get object properties
rename (compartment, parameter, species, reaction)Rename object and update expressions
set (any object)Set object properties

Property Summary

Properties for species objects

BoundaryConditionIndicate species boundary condition
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
UserDataSpecify data to associate with object
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