2011 - Athens - Greece

PAGE 2011: Software demonstration
Joakim Nyberg

PopED - An optimal experimental design software

Joakim Nyberg, Sebastian Ueckert, Eric Str÷mberg, Mats O. Karlsson and Andrew C. Hooker

Department of Pharmaceutical Biosciences, Uppsala University, Sweden

PopED is an Optimal Experimental Design tool for Non-Linear Mixed Effect Models [1].  Key features of PopED include the ability to optimize over multiple possible models as well as to assume distributions around model parameter values (ED-optimal design). For the latter PopED can use asymptotically exact Monte-Carlo methods or faster performing Laplace approximations for the integration step. PopED allows the user to optimize over any design variable (sample times, doses, number of individuals, start and stop time of experiments, infusion lengths, etc...) greatly enhancing the information content of experiments. Furthermore, PopED can optimize using penalty functions allowing for power optimization, cost optimization, optimization of discrete type data, time-to-event models etc. In addition, the computations can be  executed in parallel using Open MPI [2] or Matlab Parallel Compiler Toolbox [3].

PopED consists of two parts, a script version, responsible for all optimal design calculations, and a Graphical User Interface (GUI), facilitating the setup of an optimization task for users. The script version can use either Matlab [3] or Freemat [4] (a free alternative to Matlab) as an underlying engine. The GUI is a window based application written in C# that can be run with .NET 2.0 (MS Windows) or with Mono (Linux/MacOS). In addition to easing the implementation of an experimental design optimization, the GUI also provides model templates, examples, tools for interpretation of the optimal design outcome and ways to validate and simulate models prior to optimization. All these tools are also accessible via the script version of PopED. PopED is freely available at poped.sf.net.

1. Foracchia, M., et al., POPED, a software for optimal experiment design in population kinetics. Comput Methods Programs Biomed, 2004. 74(1): p. 29-46.
2. Open MPI, version 1.4.3 (2010) http://www.open-mpi.org/
3. Matlab, version 7.4 - 7.10 (2007-2010) http://www.mathworks.com/
4. Freemat, version 4.0 (2009) http://freemat.sourceforge.net

Reference: PAGE 20 (2011) Abstr 2231 [www.page-meeting.org/?abstract=2231]
Software demonstration