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Abstract for Seminar
This talk presents an approach based on ``Executable Biology'' (also called ``Algorithmic Systems/Synthetic Biology'') for the specification, analysis and execution of programs for living entities. The methodology consists of the formal specification of programs for individual (proto)cells as stochastic P systems. These specifications can be made modular through the use of libraries of modules representing recurrent biological motifs or well-characterised synthetic biological parts, e.g. transcriptional logic gates, that can be reused in different contexts. A second level of modularity is afforded by the specification of individual cells, which can then be distributed in space describing different topological arrangements for multi cellular systems. Specifications are then executed with multi-compartmental Gillespie-like algorithms and Dissipative Particle dynamics. I will describe wet lab experimental validations and, time permitting, briefly mention challenges and opportunities for computer scientists.