SBML Compatibility
The Systems Biology Toolbox 2 allows to import Level 1 and 2 SBML models. The export to SBML is only available
to generate Level 2 SBML models. The import is based on the TranslateSBML function provided by the
libSBML and SBMLToolbox package.
Export of SBML models is based on the OutputSBML function.
The correctness of the import of SBML models has been verfied by checking the involved functions against the Semantic Test Suite on SBML.ORG. Limitations of the import and necessary assumptions are listed below.
Limitations of the import of SBML models
SBML Level 1 and 2
- The use of units and their definitions is not considered.
Assumptions made when importing SBML models
When importing SBML models several assumptions had to be made.
SBML Level 1
Since no distinction between amounts and concentrations is possible in SBML Level 1, the initial values for the species are assumed to be given in amounts and converted to concentrations by dividing with the compartment size of the compartment in which the species are in. According to the SBML standard kinetic rate laws are assumed to have units amount/time and the species appearing in the rate laws are assumed to have concentration units.In models that have only compartments of a constant size of 1 the distinction between amounts and concentrations is not necessary.
The values of the species in the MATLAB representation of the model will be in concentration units.
SBML Level 2
When importing SBML Level 2 models species for which the initial value is given as initialAmount and hasOnlySubstanceUnits is set to true (or compartment dimension is zero) are treated as amounts. If hasOnlySubstanceUnits is set to false but the initial value is given as amount the corresponding species are converted to concentration. Species for which the initial value is given as initialConcentration are treated as concentrations. It is then assumed that the value of species appearing in the kinetic rate laws have either amount or concentration units. All rules are evaluated as given by the SBML model. According to the SBML standard rate laws of reactions are assumed to deliver a rate in amount/time. In the case a species value is defined as concentration the rate law is converted to concentration/time.In models that have only compartments of a constant size of 1 the distinction between amounts and concentrations is not necessary.
Limitation of the export of SBML models
Export of SBmodels is only done to SBML Level 2 Version 1. Species given by amount units will obtain a hasOnlySubstanceUnits flag that is set to true in the SBML file.
