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Targeted Development of Registries of Biological Parts
BACKGROUND: The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Stand...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441434/ https://www.ncbi.nlm.nih.gov/pubmed/18628824 http://dx.doi.org/10.1371/journal.pone.0002671 |
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author | Peccoud, Jean Blauvelt, Megan F. Cai, Yizhi Cooper, Kristal L. Crasta, Oswald DeLalla, Emily C. Evans, Clive Folkerts, Otto Lyons, Blair M. Mane, Shrinivasrao P. Shelton, Rebecca Sweede, Matthew A. Waldon, Sally A. |
author_facet | Peccoud, Jean Blauvelt, Megan F. Cai, Yizhi Cooper, Kristal L. Crasta, Oswald DeLalla, Emily C. Evans, Clive Folkerts, Otto Lyons, Blair M. Mane, Shrinivasrao P. Shelton, Rebecca Sweede, Matthew A. Waldon, Sally A. |
author_sort | Peccoud, Jean |
collection | PubMed |
description | BACKGROUND: The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. METHODS/PRINCIPAL FINDINGS: By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. CONCLUSIONS/SIGNIFICANCE: Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users. |
format | Text |
id | pubmed-2441434 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-24414342008-07-16 Targeted Development of Registries of Biological Parts Peccoud, Jean Blauvelt, Megan F. Cai, Yizhi Cooper, Kristal L. Crasta, Oswald DeLalla, Emily C. Evans, Clive Folkerts, Otto Lyons, Blair M. Mane, Shrinivasrao P. Shelton, Rebecca Sweede, Matthew A. Waldon, Sally A. PLoS One Research Article BACKGROUND: The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. METHODS/PRINCIPAL FINDINGS: By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. CONCLUSIONS/SIGNIFICANCE: Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users. Public Library of Science 2008-07-16 /pmc/articles/PMC2441434/ /pubmed/18628824 http://dx.doi.org/10.1371/journal.pone.0002671 Text en Peccoud et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Peccoud, Jean Blauvelt, Megan F. Cai, Yizhi Cooper, Kristal L. Crasta, Oswald DeLalla, Emily C. Evans, Clive Folkerts, Otto Lyons, Blair M. Mane, Shrinivasrao P. Shelton, Rebecca Sweede, Matthew A. Waldon, Sally A. Targeted Development of Registries of Biological Parts |
title | Targeted Development of Registries of Biological Parts |
title_full | Targeted Development of Registries of Biological Parts |
title_fullStr | Targeted Development of Registries of Biological Parts |
title_full_unstemmed | Targeted Development of Registries of Biological Parts |
title_short | Targeted Development of Registries of Biological Parts |
title_sort | targeted development of registries of biological parts |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441434/ https://www.ncbi.nlm.nih.gov/pubmed/18628824 http://dx.doi.org/10.1371/journal.pone.0002671 |
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