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article

Virtual test tubes

Authors:

Derrel R. Blain,

Andrew J. NeelAuthors Info & Claims

Natural Computing: an international journal, Volume 3, Issue 4

Pages 461 - 477

Published: 01 December 2004 Publication History

Abstract

By their structure and operation, biomolecules have resolved fundamental problems as a distributed computational system that we are just beginning to unveil. One advantageous approach to gain a good understanding of the processes and algorithms involved is simulation on conventional computers. Simulations allow better understanding of the capabilities of molecules because they can occur at the level of reliability, efficiency, and programmability that are standard in conventional computation and are desirable for experiments in vitro . Here, we describe in some detail the architecture of a general-purpose simulation environment in silico , EdnaCo, establish its soundness and reliability, and benchmark its performance. The system can be described as an emulation of the events in a real test tube. We describe the major pieces of its architecture, namely, a distributed memory (file) system, a kinetic engine, and input/output mechanisms. Finally, the ability of this environment in preserving major features of the wet counterpart in vitro is evaluated via an implementation on a cluster of PCs. The results of several simulations are summarized that establish the soundness, utility, applicability, and cost efficiency of the software to facilitate experimentation in vitro .

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Cited By

Garzon M(2012)Theory and applications of DNA codeword designProceedings of the First international conference on Theory and Practice of Natural Computing10.1007/978-3-642-33860-1_2(11-26)Online publication date: 2-Oct-2012
https://dl.acm.org/doi/10.1007/978-3-642-33860-1_2
Garzon MWong T(2011)DNA chips for species identification and biological phylogeniesNatural Computing: an international journal10.1007/s11047-010-9232-y10:1(375-389)Online publication date: 1-Mar-2011
https://dl.acm.org/doi/10.1007/s11047-010-9232-y
Garzon MWong T(2010)Search and validation of short genome-wide biomarkers for bacterial biological phylogeniesProceedings of the 16th international conference on DNA computing and molecular programming10.5555/1949977.1949982(49-58)Online publication date: 14-Jun-2010
https://dl.acm.org/doi/10.5555/1949977.1949982
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Published In

cover image Natural Computing: an international journal

Natural Computing: an international journal Volume 3, Issue 4

December 2004

118 pages

ISSN:1567-7818

Issue’s Table of Contents

Copyright © Copyright © 2004 Kluwer Academic Publishers.

Publisher

Kluwer Academic Publishers

United States

Publication History

Published: 01 December 2004

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Cited By

Garzon M(2012)Theory and applications of DNA codeword designProceedings of the First international conference on Theory and Practice of Natural Computing10.1007/978-3-642-33860-1_2(11-26)Online publication date: 2-Oct-2012
https://dl.acm.org/doi/10.1007/978-3-642-33860-1_2
Garzon MWong T(2011)DNA chips for species identification and biological phylogeniesNatural Computing: an international journal10.1007/s11047-010-9232-y10:1(375-389)Online publication date: 1-Mar-2011
https://dl.acm.org/doi/10.1007/s11047-010-9232-y
Garzon MWong T(2010)Search and validation of short genome-wide biomarkers for bacterial biological phylogeniesProceedings of the 16th international conference on DNA computing and molecular programming10.5555/1949977.1949982(49-58)Online publication date: 14-Jun-2010
https://dl.acm.org/doi/10.5555/1949977.1949982
Garzon MPhan VRoy SNeel A(2006)In search of optimal codes for DNA computingProceedings of the 12th international conference on DNA Computing10.1007/11925903_11(143-156)Online publication date: 5-Jun-2006
https://dl.acm.org/doi/10.1007/11925903_11

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