Computational analysis and model integration of biorhythmic systems

Bc. Jakub Šalagovič

Master's thesis

Abstract:

Táto práca sa zaoberá integráciou modelu a analýzou modelu vytvoreného spojením mechanizmu cirkadiálnych rytmov a metabolizmu uhlíku a dusíku v prokaryotickom organizme – siniciach. Pre dosiahnutie toho bolo potrebné urobiť rešerš existujúcich matematických modelov pokrývajúcich daný fenomén. Po zvolení najvhodnejších modelov sme identifikovali a modelovali ich samotné spojenie. Spolu s novovytvoreným integrovaným modelom boli vybrané modely implementované na platforme E-cyanobacterium.org. Následne bolo analyzované oscilačné chovanie navrhnutého integrovaného modelu pomocou simulácie a formálnych metód.

Abstract:

This thesis deals with model integration and an analysis of model created connecting a circadian clock and a carbon-nitrogen metabolism in the prokaryotic organisms of cyanobacteria. To do so, a review of existing mathematical models covering selected phenomena was needed. Once the most suitable models had been selected, we identified and modelled their possible connection. Together with a newly created integrated model, the selected models were implemented on the E-cyanobacterium.org platform. The oscillatory behaviour of the proposed integrated model was subsequently analysed in terms of simulation and formal methods.

Keywords

systems biology, biorhythms, circadian clock, metabolism, model integration, formal analysis, monitoring, simulation, systémová biológia, biorytmy, cirkadiálne hodinky, metabolizmus, integrácia modelu, formálna analýza, simulácia

Language used: English

Date on which the thesis was submitted / produced: 12. 12. 2017

Thesis defence

• Date of defence: 5. 2. 2018
• Supervisor: RNDr. David Šafránek, Ph.D.
• Reader: Ing. Jan Červený, Ph.D.

Masaryk University

Faculty of Informatics

Master programme / field:
Applied Informatics / Bioinformatics