Executable Biology

Jasmin Fisher and Thomas A. Henzinger

Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models --mathematical and computational-- according to their different representations of biological phenomena and their diverse potential. 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 give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.

Proceedings of the Winter Simulation Conference (WSC), IEEE Computer Society Press, 2006, pp. 1675-1682.

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