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Executable cell biology

Abstract

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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Figure 1: The methodology of executable biology.
Figure 2: Boolean networks.
Figure 3: Petri nets.
Figure 4: Interacting state machine models.
Figure 5: Pi calculus.
Figure 6: Hybrid systems.
Figure 7: The analogy between hardware design and biological models.

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Acknowledgements

We apologize to colleagues whose work was not reviewed due to lack of space. We thank John K. Heath, Alex Hajnal, Freddy Radtke and Nir Piterman for helpful discussions and critical readings of the manuscript and the anonymous referees for valuable comments. J.F. is particularly grateful to David Harel for introducing her to this line of research and for many fruitful discussions over the years. Our research is supported in part by the Swiss National Science Foundation under grant 205321-111840.

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Correspondence to Jasmin Fisher or Thomas A Henzinger.

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Fisher, J., Henzinger, T. Executable cell biology. Nat Biotechnol 25, 1239–1249 (2007). https://doi.org/10.1038/nbt1356

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