Programming in Biomolecular Computation

Hartmann, Lars; Jones, Neil D.; Simonsen, Jakob Grue

doi:10.1016/j.entcs.2010.12.008

Cited by 3 publications

(4 citation statements)

References 27 publications

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“…This universality prompted us to ask the question Where are the programs? Our recent work [67,68] tries to answer this question, where we presented the outline of a computation model that seems biologically more plausible than existing silicon-inspired models. We hope that it sets a standard for a biological device that can be both universal and programmable.…”

Section: Discussionmentioning

confidence: 99%

“…In [67,68] we propose a specific instruction set. Here we include a subset of the instructions for illustration.…”

Section: The Blob Model Of Programmed Universal Computationmentioning

confidence: 99%

“…Recent work involves programming a blob simulator, and execution visualiser. Prototype implementations of both have been made, described in [67,68].…”

Section: What Can Be Done In the Blob World?mentioning

confidence: 99%

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Computational Biology: A Programming Perspective

Hartmann

Jones

Simonsen

et al. 2011

Formal Modeling: Actors, Open Systems, Biological Systems

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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 programmingrelated 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. ContextThe terms "biocomputing" and "systems biology", taken in their broadest senses, span many fields and areas of research: biology, chemistry, physics, mathematics, electrical engineering and computer science among others. Two major subareas:-Computer modeling of biological and biomolecular processes -Biological hardware for computationThe terms "biomolecular computation" and "biomolecular computational model" occur with both meanings in the literature (see Section 4), sometimes referring to the one and sometimes the other subarea. This paper emphasises the second. More precisely: we take a synthetic viewpoint, concerned with building things as in the engineering and computer sciences. This is in contrast to the inevitable and ubiquitous analytic viewpoint common to the natural sciences, concerned with finding out how naturally evolved things work. We ask: What can be done or built or constructed; and not: how does nature work? (Caveat: just as in engineering, one will need to understand nature's cause-and-effect sufficiently well to be able to modulate it, i.e., to use nature to effectively serve our purposes.) A Theme: Biological Problem-SolvingOur main aim is thus to use the biological world as a computational medium. From a programming perspective, the main goal is problem-solving by writing programs. This section thus refers to solving problems by biology, not solving problems about biology or in biology.Given: a computational problem. To find: a biological solution. Further, problem-solving by a program means finding a general solution (and not just one run of one algorithm on one input data instance).A top-down approach is to devise a model of computation that -satisfies requirements for computer science/engineering -that could conceivably be realised in a biological medium -in which programs are clearly visible, and programming can be done -is a framework in which it is possible, at least in principle, to say when a problem has be...

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Section: Discussionmentioning

confidence: 99%

“…In [67,68] we propose a specific instruction set. Here we include a subset of the instructions for illustration.…”

Section: The Blob Model Of Programmed Universal Computationmentioning

confidence: 99%

See 1 more Smart Citation

Computational Biology: A Programming Perspective

Hartmann

Jones

Simonsen

et al. 2011

Formal Modeling: Actors, Open Systems, Biological Systems

Self Cite

View full text Add to dashboard Cite

show abstract

“…In most of these approaches, the underlying principle is to get inspiration from concrete chemical phenomenon in order to derive abstract models of computation which are potentially usable. This includes the model of biomolecular computation [198], the Chemical Abstract Machine [54], Membrane Computing models [273], Biochemical Ground Form process algebra's approaches [109], DNA based computation models [287], or Chemical Reaction Networks (CRN) discussed in Section 6.5.…”

Section: Dna and Molecular Computingmentioning

confidence: 99%