Benchmark: SBPD vs. ODE15S

To display the improvement of the simulation speed, obtained through SBPD in comparison to the fastest MATLAB solver ODE15S, a benchmark was performed for three different models. The computer used was a DELL Latitude D610, Centrino 2GHz, 512MB RAM 800MHz, Windows XP.

As compiler for the MEX files MinGW was used, that is available in the SBTOOLBOX2 distribution.

The MATLAB script that was used is available in the SBPD distributions example folder.

Model 1Model 2Model 3
 
Model description Novak Tyson cell-cycle model Full-scale model of glycolysis in yeast Model 14 from the Biomodels.net database
End time (TEND) 100050300
Number simulation
points (NRPOINTS)
1000200300
 
Average time
ODE15S [ms]
34423448743
Average time
SBPD [ms]
246824
 
Speedup by SBPD 144x51x30x

 

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