Parameter Discovery for Biological Models Using Model Checking
Current challenges in computational systems biology call for new insights coming from computer science, especially, the field of formal methods. This is motivated by the need for model-based computational analysis and exploration of hardly-predictable behaviour emerging from complex biological systems. The discovery of kinetic constants and other model parameters is an essential part of the typical research cycle in systems biology. The direct measurement of parameters through wet-lab experiments is often difficult or even impracticable. The proposed project primarily aims at development of new automated techniques for parameter synthesis based on fitting the computerized model to a temporal logic hypothesis. The proposed methodology uses the model checking method as known from formal verification of computer systems. In order to achieve scalability, a special emphasis is given to the development of parallel algorithms.
The goal of the project is to develop new computer-scientific techniques for automated parameter synthesis from temporal logic hypotheses. The project primarily aims at the research of original high-performance techniques for discovering robust parametrizations of large-scale biological models.
Innovation of Bachelor's and Master's field of study Bioinformatics in the direction of System Biology has been co-financed by European Social Fund and Ministry of Education, Youth and Sports of the Czech Republic project. The project has been implemented in collaboration with an industrial partner - Photon Systems Instruments, spol. s r.o..