Profile Likelihood Exploit

This approach is described in detail in:
Raue A., Kreutz C., Maiwald T., Bachmann J., Schilling M., Klingmüller U. and Timmer J. (2009) Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics, 25(15), 1923-1929. doi:10.1093/bioinformatics/btp358

Installation: This implementation is embedded within the PottersWheel modeling and multi-experiment fitting toolbox (Maiwald and Timmer, Bioinformatics 2008) for MATLAB. The package is distributed in combination with the PottersWheel toolbox since version 2.0, which can be downloaded free of charge for scientific purposes from the PottersWheel homepage. If you are not familiar with the PottersWheel environment, please read the corresponding user manual or try to follow the example described in the PLE manual.

PLE manual: PLE-Manual-Version-2010-01-21.pdf

Example described in the manual: example.zip

Showcase model from the publication: jak-stat.zip

Update: Please copy the following files into the PottersWheel subfolder Plugins/PLE/ and replace the existing files.

PLE Update 2010-02-01: ple-update.zip

Usage: It is highly recommended to use PottersWheel later than 2.0.40 where the sundials 2.4.0 ODE solver package is supported (see also pwInstallSundialsTB). It facilitates a numerically more reliable calculation of the profile likelihood. The recommended setting can be assigned in the configuration panel of PottersWheel by:

- fields > integration -> integrator = 14 (CVODES)
- fields > integration -> calcJacobian = true
- fields > integration -> useJacobian = true

- fields > optimization -> method = 1 (trustregion)
- fields > optimization -> fitInLogParameterSpace = true
- fields > optimization -> calcJacobian = true
- fields > optimization -> useJacobian = true

If you prefer to work with scripts, please utilize the commands pwGetConfig and pwSetConfig. Note, that the MATLAB Symbolic Toolbox is required for the formal calculation of the Jacobian.

Feel free to contact me for support or to implement the approach within your own modeling framework.