Parameter Identification and Model Ranking of Thomas Networks

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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.
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