<<< Announcement: SBTOOLBOX2/SBPD/SBPOP is going to be renamed >>>

It was time to better document the tools available in SBPOP for modeling and simulation work in the pharmacometric area. The tools for systems biology, of course, have always been well documented. Along with the better documentation many improvements were introduced, requiring a reorganization of the code.

The "SB", "SBPD", and "SBPOP" prefixes for the functions in the different packages did not make sense anymore after this reorganization. Thus a new name was sought, that by not using "SB" reflects that the complete package is not only focusing on Systems Biology, but that a much wider area can be covered.

I will not make it long. Soon the www.sbtoolbox2.org webpage will be linked to IQM Tools and the distribution of SBPOP Package / SBTOOLBOX2 will be replaced by IQM Tools.

IQM Tools has the same functionality as the current SBPOP Package and adds quite some additional things. It also has been made more robust and better documented.

As the SBPOP Package also IQM Tools is distributed as open source and free of charge.

From now on, please go to: IQM Tools to download the newest version of IQM Tools.

Also check out the tutorials section (IQM Tools Tutorials), which instead of one tutorial now as six available.

The “SBPOP Package”: Efficient Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation

Model-based drug development (MBDD) emphasizes the quantitative integration of the relationships among diseases and disease targets, drug characteristics, and individual variability across studies and development phases for rational and scientifically based decision making. Within MBDD, mathematical models are used to integrate available knowledge and complex heterogeneous data to allow for hypothesis testing, design and optimization of learning experiments/studies, and subsequent confirmation or rejection, leading to increased knowledge (REF).

Model-based drug development deals with a large model space, consisting of, for example, Systems Biology/pathway, physiologically based PKPD, dose-concentration-response, and mechanism based disease models. Fast turnaround of modeling and simulation activities is crucial in order to influence the decision making process in drug development projects. Such a fast turnaround, however, requires that workflows are efficiently supported by powerful and user-friendly tools.

The “SBPOP PACKAGE” has been developed as a toolbox for the widely used general purpose mathematical software MATLAB. It consists of three parts: SBTOOLBOX2, SBPD, and SBPOP. The first two parts are widely used in the area of Systems Biology, implementing functionality for general representation of dynamic models, simulation, analysis, parameter estimation, and high performance simulation. While these parts are ideal for the support of data and information integration in the research and preclinical phases of the drug discovery and development process, the third part (SBPOP) adds seamless functionality for data analysis and exploration, population PK/PD modeling, and clinical trial simulation. An important focus in the development has been on user friendliness, documentation, training material, and extensibility.

The “SBPOP PACKAGE” is continuously developed further to include additional analyses and workflows of standard modeling approaches. The development is driven by real needs in real drug development projects, with the goal to increase efficiency, allowing for timely feedback of results and insights to the decision making process.
 
 
 
 

 

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