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Model Checking of Biological Systems

David Safranek ( Masaryk University, Czech Republic )

The goal of computational systems biology is to develop models that can predict and explain uknown facts about the dynamics of biological systems, especially, non-trivial behaviour emerging from the interplay among the enormous number of individual biochemical components. The models are based on known first principles, wet-lab measurements, and existing hypotheses available in literature. A lot of information remains unknown, e.g., quantitative parameters such as rates of individual biochemical events.

All the known or expected biological facts can be formalized in temporal logics. Model checking techniques known from formal verification can be then used to explore models with respect to a given set of temporal properties (dynamical constraints). The space of uncertainty in models can be then restricted by means of these constraints. This gives the modellers a powerful alternative to traditional parameter fitting methods.

In this talk, an overview of applications of model checking to biological models will be given. In particular, we will focus on deterministic models -- traditional differential (kinetic) models and their discrete abstractions. Two case studies of applying model checking to biological systems will be presented, in particular, gene regulation of mammalian cell cycle and ammonium transport in E. coli.

Speaker bio

David Safranek received his M.S. Degree in computer science at Masaryk University, Czech Republic in 2001. He completed his Ph.D. thesis in the area of formal specification of concurrent systems at the same university in 2006. During Ph.D. he spent one semester at Faculty of Computer Science, University of Namur, Belgium. In the period 2007-2010 he worked as a postdoc associated to the FP6-NEST project EC-MOAN (E.Coli Modelling and Analysis) where he collaborated with highly acclaimed experts in systems biology, e.g., Hans Westerhoff, Igor Goryanin, and Hidde de Jong.

Currently he has a position of assistant professor at Faculty of Informatics, Masaryk university where he works as a research assistant at Systems Biology Laboratory and as a lecturer of computer science and systems biology. He is a co-founder of the new study branch devoted to the interdisciplinary field of systems biology. In his current research, David Safranek primarily focuses on applications of formal methods to systems biology

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