Computational biology: a programming perspective

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 -