A List by Author: David Šafránek
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Parameter Identification and Model Ranking of Thomas Networks
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
A visual formalism called Visual Coordination Diagrams (VCD)
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