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.
|addspecies (model, compartment)||Create species object and add to compartment object within model object|
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|
|get (any object)||Get object properties|
|rename (compartment, parameter, species, reaction)||Rename object and update expressions|
|set (any object)||Set object properties|
Properties for species objects
|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 SimBiology object type|
|UserData||Specify data to associate with object|