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

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.

 

SBPOP PUBLICATIONS

Publications, discussing results obtained with the help of the SBPOP PACKAGE, are asked to reference the most relevant of the following papers and additionally the link to this webpage:

  • Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515, 2006, doi:10.1093/bioinformatics/bti799
  • SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB, Bioinformatics, 23(5), 646-647, 2007, doi:10.1093/bioinformatics/btl668
  • SBPOP Package: Efficient support for model based drug development from mechanistic models to complex trial simulation, PAGE meeting, Glasgow, UK [abstract]
  • Enhancing population pharmacokinetic modeling efficiency and quality using an integrated workflow, Journal of Pharmacokinetics and Pharmacodynamics, doi:10.1007/s10928-014-9370-4, 2014.
SBPOP NEWS
  • 16th March 2015: Many small improvements ... also SBML export now fully working again
  • 20th January 2015: Many improvements ... Windows 64bit support and compatibility with MATLAB versions >=R2014B
  • 28th July 2014: Happy to announce that our paper about efficient conduct of popPK anlalyses has been published (doi:10.1007/s10928-014-9370-4)
  • 3rd July 2014: Update to Revision 1361 (due to packaging bug in Rev 1352)
  • 18th June 2014: Update to Revision 1352 (popPK modeling workflow MONOLIX and NONMEM, "median" modeling support)
  • 25th March 2014: Update to Revision 1278
  • 7th May 2013: Revision 1172 had a minor bug due to packaging of the public version - main impact on running SBPDgui. Fixed now in Revision 1176
  • 2nd May 2013: SBTOOLBOX2 and SBPD are now integrated into the same package, called "SBPOP PACKAGE". The new combined package additionally includes "SBPOP", focusing on PK/PKPD/PBPK models, population modeling, nonlinear mixed effect parameter estimation, clinical trial simulation