Technical Reports

A List by Author: David Šafránek

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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.

VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures

by David Šafránek, Jiří Šimša, A full version of SOFSEM 2005 paper. December 2004, 25 pages.

FIMU-RS-2004-11. Available as Postscript, PDF.


A visual formalism called Visual Coordination Diagrams (VCD) for high-level design of heterogeneous systems is presented in this paper. The language is based on a state-transition operational semantics, which allows application of formal methods to software design. Formal definition of VCD is included in the paper. Moreover, an example of use of the language is also given.

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