Targeted Development of Registries of Biological Parts

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dc.contributorVirginia Techen
dc.contributor.authorPeccoud, Jeanen
dc.contributor.authorBlauvelt, Megan F.en
dc.contributor.authorCai, Yizhien
dc.contributor.authorCooper, Kristal L.en
dc.contributor.authorCrasta, Oswalden
dc.contributor.authorDeLalla, Emily C.en
dc.contributor.authorEvans, Cliveen
dc.contributor.authorFolkerts, Ottoen
dc.contributor.authorLyons, Blair M.en
dc.contributor.authorMane, Shrinivasrao P.en
dc.contributor.authorShelton, Rebeccaen
dc.contributor.authorSweede, Matthew A.en
dc.contributor.authorWaldon, Sally A.en
dc.date.accessed2014-05-06en
dc.date.accessioned2014-06-17T20:12:03Zen
dc.date.available2014-06-17T20:12:03Zen
dc.date.issued2008-07-16en
dc.description.abstractThe 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.en
dc.description.sponsorshipThis work was supported by the Commonwealth of Virginia Research Initiative. YC was supported by a fellowship from the Genetics, Bioinformatics, and Computational Biology program at Virginia Tech. RS was supported by a fellowship from the Bradley Department of Electrical and Computer Engineering. None of the sponsors were involved in the design of this work or analysis of the data.en
dc.identifier.citationPeccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, Waldon SA (2008) Targeted development of registries of biological parts. PLoS One 3(7): e2671.en
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0002671en
dc.identifier.issn1932-6203en
dc.identifier.urihttp://hdl.handle.net/10919/48968en
dc.identifier.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002671en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectDNA sequence analysisen
dc.subjectDNA sequencesen
dc.subjectPolymerase chain reactionen
dc.subjectSequence alignmenten
dc.subjectSequence analysisen
dc.subjectSequence assembly toolsen
dc.subjectSequence databasesen
dc.subjectSynthetic biologyen
dc.titleTargeted Development of Registries of Biological Partsen
dc.title.serialPLoS ONEen
dc.typeArticle - Refereeden

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