Parameter Identification and Model Ranking of Thomas Networks

Investor logo

Warning

This publication doesn't include Faculty of Sports Studies. It includes Faculty of Informatics. Official publication website can be found on muni.cz.
Authors

KLARNER Hannes STRECK Adam ŠAFRÁNEK David KOLČÁK Juraj SIEBERT Heike

Year of publication 2012
Type Article in Proceedings
Conference Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings
MU Faculty or unit

Faculty of Informatics

Citation
Web http://link.springer.com/chapter/10.1007/978-3-642-33636-2_13
Doi http://dx.doi.org/10.1007/978-3-642-33636-2_13
Field Informatics
Keywords Thomas network; parameter identification; model checking
Description We propose a new methodology for identification and analysis of discrete gene networks as defined by René Thomas, supported by a tool chain: (i) given a Thomas network with partially known kinetic parameters, we reduce the number of acceptable parametrizations to those that fit time-series measurements and reflect other known constraints by an improved technique of coloured LTL model checking performing efficiently on Thomas networks in distributed environment; (ii) we introduce classification of acceptable parametrizations to identify most optimal ones; (iii) we propose two ways of visualising parametrizations dynamics wrt time-series data. Finally, computational efficiency is evaluated and the methodology is validated on bacteriophage \lambda case study.
Related projects:

You are running an old browser version. We recommend updating your browser to its latest version.

More info