Systems Biology Markup Language (SBML) is a standard format for sharing systems biology models
among various modeling and simulation software tools. The current specification is available
Import an SBML model from a file or URL using
SimBiology® supports a subset of the SBML level 3 version 1 specification. The following SBML features are not imported into the SimBiology model:
Piecewise kinetics — Models with piecewise kinetics are loaded, but the definitions for piecewise kinetics are ignored.
MATLAB® incompatible variable names in
Models that have variable names incompatible with MATLAB in
not loaded and an error message is displayed.
hasOnlySubstanceUnits attribute does not have a corresponding property
in the SimBiology species object. Instead, if the species has no units, SimBiology uses the
DefaultSpeciesDimension property to
determine whether to interpret species names in expressions as substance amounts or
concentrations. When you set
substance and do not specify units, SimBiology interprets species
names as substance amounts and does not scale by any compartment capacity (volume). When
the property is set to
concentration, species names are interpreted
as concentrations and are scaled by the appropriate compartment capacity. SimBiology
does not let you set the initial value of a species as concentration or substance amount
independently of how you refer to it in expressions. To provide better compatibility
with SBML models having this attribute, SimBiology adds an initial assignment rule or
appropriate units during the import process. For details, see the Compatibility section of
Models containing other models as submodels are loaded but submodels are ignored.
fast attribute of any reaction
object is ignored.
persistent attributes of event objects are
operators having three or more arguments are not supported. They are
supported for binary operations only.
You can import SBML models with function definitions. SimBiology replaces the function definitions with the corresponding mathematical expressions.
You can also load SBML models that use reaction IDs to reference reaction rates in mathematical expressions. SimBiology replaces the references with the corresponding reaction rates.
The following SimBiology model information is included in the SBML format file:
Compartments, species, parameters, reactions, rules,
and events that are defined in the model and have their
All unit definitions in SBML-compliant format.
Model component properties with SBML equivalents, such as notes, and unit values for species and parameters.
The reaction rate equation, but not the kinetic law definition.
The following SimBiology features are not supported by
SBML and are not included in the saved SBML format file. You can store
this information in a SimBiology project file, which has an
Projects — Models, analysis tasks, and data.
Kinetic law information — SimBiology models store kinetic law information such as the kinetic law name and a kinetic law definition.
Variant information — Collections of quantities (compartments, species, and/or parameters) that you can use to alter a model's initial or base configuration.
Dosing information — Exogenous increments to the amount (or concentration) of a species in a model.
Custom MATLAB function files — Custom functions that you used in your SimBiology model.
Features and properties specific to SimBiology software,
such as Name (of
only), Tag, and Active.
Because the previous information is not supported by SBML, we recommend saving SimBiology project files to capture this information.