SimBiology and SBML :: Introduction (SimBiology®)

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

Because SimBiology supports a subset of the SBML Level 2 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.
Function definitions — Models containing function definitions are loaded, but a warning is displayed, and the function definitions 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 field does not have a corresponding property in the SimBiology species object. For more information on dimensions for SimBiology species, see DefaultSpeciesDimension.

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, V_m*S/(K_m+S), is a definition stored in the Kinetic Laws library. Specifically, for a one-substrate enzyme-catalyzed reaction, if you assign V_m = V_a, K_m = K_a, and S = A, then the reaction rate equation is exported to SBML as V_a*S/(K_a+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.
Features and properties specific to SimBiology software, such as Tag and Active.

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

Using the SimBiology Desktop vs. the Command Line

Getting Started Using the SimBiology Desktop

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