Stefano Schivo EWI-FMT University of Twente P.O. Box 217 7500 AE Enschede The Netherlands Phone: +31 (0)53 489 3979 Fax: +31 (0)53 489 3247 Email: Office: Zilverling 5033

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Since November 2010 I am a post-doc at the University of Twente, working on modelling biological pathways with Timed Automata. The project aims at producing a framework to quantitatively model the interactions happening inside biological cells. In particular, the current target is the dynamic evolution of kinase pathways, which are the mechanisms underlying the cellular response to external signals such as growth and death factors. The formal foundation of the framework rests on Timed Automata, and models are checked against experimental data thanks to the powerful tool UPPAAL. The Timed Automata formalism is hidden behind a user interface based on Cytoscape, a widely spread program used in modeling biological interactions. This makes it easy for the molecular biologist to test and formulate hypotheses about a specific kinase network without needing any knowledge about the underlying formal model.