Technical Reports

A List by Author: Heike Siebert

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Parameter Identification and Model Ranking of Thomas Networks

by Hannes Klarner, Adam Streck, David Šafránek, Juraj Kolcak, Heike Siebert, A full version of the paper presented at conference CMSB 2012. November 2012, 39 pages.

FIMU-RS-2012-03. Available as Postscript, PDF.


We propose a new methodology for identification and analysis of discrete gene networks as defined by Rene 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 the most optimal ones; (iii) we propose a way of visualising parametrizations dynamics wrt time-series data. The methodology is validated on a rat neural development case study; (iv) finally we provide description of developed algorithms and evaluation of their performance.

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