Computational biology: a programming perspective

Lars Røeboe Hartmann; Neil Jones; Jakob Grue Simonsen; Søren Bjerregaard Vrist

doi:10.1007/978-3-642-24933-4_20

Computational biology: a programming perspective

Lars Røeboe Hartmann, Neil Jones, Jakob Grue Simonsen, Søren Bjerregaard Vrist

2 Citations (Scopus)

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.

Original language	English
Title of host publication	Formal modeling : actors, open systems, biological systems
Editors	Gul Agha, Olivier Danvy, José Meseguer
Number of pages	31
Publisher	Springer
Publication date	2011
Pages	403-433
ISBN (Print)	978-3-642-24932-7
ISBN (Electronic)	978-3-642-24933-4
DOIs	https://doi.org/10.1007/978-3-642-24933-4_20
Publication status	Published - 2011

Series	Lecture notes in computer science
Volume	7000
ISSN	0302-9743

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Computational biology: a programming perspective. / Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue et al.
Formal modeling: actors, open systems, biological systems. ed. / Gul Agha; Olivier Danvy; José Meseguer. Springer, 2011. p. 403-433 (Lecture notes in computer science, Vol. 7000).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

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Computational biology: a programming perspective

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