Computational biology: a programming perspective
Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt
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Computational biology : a programming perspective. / Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue; Vrist, Søren Bjerregaard.
Formal modeling: actors, open systems, biological systems. red. / Gul Agha; Olivier Danvy; José Meseguer. Springer, 2011. s. 403-433 (Lecture notes in computer science, Bind 7000).Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › fagfællebedømt
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TY - CHAP
T1 - Computational biology
T2 - a programming perspective
AU - Hartmann, Lars Røeboe
AU - Jones, Neil
AU - Simonsen, Jakob Grue
AU - Vrist, Søren Bjerregaard
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
U2 - 10.1007/978-3-642-24933-4_20
DO - 10.1007/978-3-642-24933-4_20
M3 - Book chapter
SN - 978-3-642-24932-7
T3 - Lecture notes in computer science
SP - 403
EP - 433
BT - Formal modeling
A2 - Agha, Gul
A2 - Danvy, Olivier
A2 - Meseguer, José
PB - Springer
ER -
ID: 170211794