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The executable pathway to biological networks

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Abstract: Computational modelling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviours. ‘Executable Biology’ is a pioneering approach focused on the design of executable computer programs that mimic biological phenomena. While traditional mechanistic models in biology are usually described by diagrams (giving a fairly static picture of cellular processes), executable biology seeks to translate such static diagrams into dynamic models using formal computational methods that were originally designed for the construction and analysis of complex man-made systems (e.g., computers and computer programs). In this talk, I will illustrate the usefulness of this framework through our group’s efforts to use Boolean Networks, Process Calculi, Live Sequence Charts, and Interacting State Machines to model signalling pathways governing normal animal development and disease, organogenesis, and immunodominance. If time permits, I will also highlight some of the main challenges that executable biology poses for Biology and Computer Science.

Biography: Jasmin Fisher is a Researcher in the Computational Science Lab at Microsoft Research Cambridge. She holds a Ph.D. degree in Neuroimmunology from the Weizmann Institute of Science and was previously (2003-2004) a postdoctoral fellow in the department of Computer Science at the Weizmann Institute, where she worked with Prof. David Harel, and then (2004-2007) a postdoctoral researcher in the School of Computer Science at the EPFL working with Prof. Tom Henzinger. Her research focuses on the applications of formal methods to biological modelling, as well as on the development of novel formalisms and tools to better understand complex biological systems. She is mainly interested in processes of cell fate determination and signalling networks operating during normal development and disease (e.g., cancer, diabetes, obesitiy).

This talk is part of the Microsoft Research Summer School series.

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