Review abstract


Nature Biotechnology 25, 1239 - 1249 (2007)
Published online: 7 November 2007 | doi:10.1038/nbt1356

Executable cell biology

Jasmin Fisher1,2 & Thomas A Henzinger2,3


Computational modeling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviors. In this review, we distinguish between two types of biological models—mathematical and computational—which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems 'executable biology', as it focuses on the design of executable computer algorithms that mimic biological phenomena. We survey the main modeling efforts in this direction, emphasize the applicability and benefits of executable models in biological research and highlight some of the challenges that executable biology poses for biology and computer science. We claim that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research. This will drive biology toward a more precise engineering discipline.

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  1. Microsoft Research, Cambridge CB3 0FB, UK.
  2. School of Computer and Communication Sciences, EPFL, Lausanne CH-1015, Switzerland.
  3. Electrical Engineering & Computer Sciences, University of California at Berkeley, California 94720-1770, USA.

Correspondence to: Jasmin Fisher1,2 e-mail: jasmin.fisher@microsoft.com

Correspondence to: Thomas A Henzinger2,3 e-mail: tah@epfl.ch.



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