SBML Support

What Is SBML?

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 at http://sbml.org/documents/.

Importing from SBML Files

Import an SBML model from a file or URL using sbmlimport.

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 UnitDefinition — Models that have variable names incompatible with MATLAB in UnitDefinition are not loaded and an error message is displayed.

• The 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 DefaultSpeciesDimension to 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 sbmlimport.

• Models containing other models as submodels are loaded but submodels are ignored.

• The fast attribute of any reaction object is ignored.

• The delay, priority, initialValue, and persistent attributes of event objects are ignored.

• XOR, OR, and AND logical operators having three or more arguments are not supported. They are supported for binary operations only.

Read-Only Support for Function Definitions

You can import SBML models with function definitions. SimBiology replaces the function definitions with the corresponding mathematical expressions.

Support for Reaction IDs

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.

Exporting a SimBiology Model to SBML Format

SimBiology Features Supported by SBML

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 Active property set to true.

• 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.

   Example

  In SimBiology, the Henri-Michaelis-Menten equation, Vm*S/(Km+S), is a definition stored in the Kinetic Laws library. Specifically, for a one-substrate enzyme-catalyzed reaction, if you assign Vm = Va, Km = Ka, and S = A, then the reaction rate equation is exported to SBML as Va*S/(Ka+A).

SimBiology Features Not Supported by SBML

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 .sbproj extension.

• 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 Rule objects only), Tag, and Active.

Tip

Because the previous information is not supported by SBML, we recommend saving SimBiology project files to capture this information.