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Executable Biology: Towards Computer Programs that Mimic Life

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Jasmin Fisher (MSR Cambridge)

The new emerging field of Systems Biology aims to gain a system-level understanding of biology. In order to achieve such an understanding we need to establish the methodologies and techniques that will enable us to understand biological phenomena in their full complexity. One such attempt is to use existing formal methods designed for the construction of computerized systems to model biological systems. We have recently shown that describing mechanistic models in a dynamic and executable language has various advantages. Dynamic models can represent phenomena of importance to biology that static models cannot represent, such as time and concurrency. In addition, formal verification methods can be used to ensure the consistency of computational models with the biological data on which they are based. In this talk, I will discuss the strength of constructing and analyzing abstract executable models in biology. This pioneering approach that I call ‘Executable Biology’ will be illustrated through different models representing signalling crosstalk during animal development. The construction and analysis of these models has provided new biological insights that were validated experimentally. If time permits, I will also discuss some of the new challenges that executable biology poses for Computer Science and Biology.

This talk is part of the Computer Laboratory Automated Reasoning Group Lunches series.

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