This package contains different types of nodes needed for
representing a substance in a biochemical pathway. Substances are
connected to reactions through connectors placed on the rim of the
circle representing the substance.
The substance models are specified by extending the partial models
of substance nodes in Substances and
adding additional attributes and equations. The Substances model is
used when the concentration in a substance node is allowed to
change without restrictions during a simulation, while BoundarySubstances
is used when the concentration can only be changed using events.
This correspond to species with the fixed or boundary attribute set
in SBML.
The AmbientSubstance
is a substance used as a reservoir in reactions. This corresponds
to the empty list of reactants or the empty list of products in an
SBML reaction. When the concentration is not determined by
reactions, the SignalSubstance
model is used. Then the substance concentration is regulated by
external equations, and it corresponds to SBML species changed by
any SBML rules.
| Name | Description |
|---|---|
| Substance | Substance with variable concentration |
| BoundarySubstance | Substance with a concentration not determined by reactions, but by events |
| AmbientSubstance | Icon for a substance used as a reservoir in reactions |
| SignalSubstance | Icon for a substance with a concentration not determined by reactions, but by external equations (translated into SBML assignments) |