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Computational Biology: A Programming Perspective

  • Chapter
Formal Modeling: Actors, Open Systems, Biological Systems

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 7000))

Abstract

Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved to be computationally universal in some sense, the full step to a bona fide programming language is rarely taken, and one question is noticeable by its absence: If the device is universal, where are the programs?

We begin with an extensive review of the literature on programming-related biocomputing; and briefly identify some strengths and shortcomings from a programming perspective. To show concretely what one could see as programming in biocomputing, we outline (from recent work) a computation model and a small programming language that are biologically more plausible than existing silicon-inspired models. Whether or not the model is biologically plausible in an absolute sense, we believe it sets a standard for a biological device that can be both universal and programmable.

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  1. Department of Computer Science (DIKU), University of Copenhagen, Denmark

    Lars Hartmann, Neil D. Jones, Jakob Grue Simonsen & Søren Bjerregaard Vrist

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    Gul Agha

  2. Department of Computer Science, Aarhus University, Abogade 34, 8200, Aarhus N, Denmark

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    José Meseguer

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Hartmann, L., Jones, N.D., Simonsen, J.G., Vrist, S.B. (2011). Computational Biology: A Programming Perspective. In: Agha, G., Danvy, O., Meseguer, J. (eds) Formal Modeling: Actors, Open Systems, Biological Systems. Lecture Notes in Computer Science, vol 7000. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24933-4_20

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