Targeted Development of Registries of Biological Parts Export

@article{citeulike:3015830, abstract = {BackgroundThe 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 FindingsBy 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/SignificanceOrganizational 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.}, address = {Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America. peccoud@vt.edu}, author = {Peccoud, Jean and Blauvelt, Megan F. and Cai, Yizhi and Cooper, Kristal L. and Crasta, Oswald and Delalla, Emily C. and Evans, Clive and Folkerts, Otto and Lyons, Blair M. and Mane, Shrinivasrao P. and Shelton, Rebecca and Sweede, Matthew A. and Waldon, Sally A.}, citeulike-article-id = {3015830}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0002671}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18628824}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18628824}, day = {16}, doi = {10.1371/journal.pone.0002671}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {biobanks, biological-effects, biological-structures, biological-substrates, combining, components, dbs, digital-libraries, extremal-biology, fdls, formal-biology, formal-digital-libraries, functionalities, genomes, homology, hyperefficiency, igem, kbs, libraries, model-organisms, modularity, modules, molecular-machines, molecular-structures, registries, repositories, reusability, sequences, synthetic-biology}, month = {July}, number = {7}, pages = {e2671+}, posted-at = {2009-05-22 18:52:21}, priority = {2}, publisher = {Public Library of Science}, title = {Targeted Development of Registries of Biological Parts}, url = {http://dx.doi.org/10.1371/journal.pone.0002671}, volume = {3}, year = {2008} }

TY - JOUR ID - citeulike:3015830 L3 - citeulike-article-id:3015830 N2 - BackgroundThe 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 FindingsBy 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/SignificanceOrganizational 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. IS - 7 JF - PLoS ONE SN - 1932-6203 AD - Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America. peccoud@vt.edu TI - Targeted Development of Registries of Biological Parts PB - Public Library of Science VL - 3 SP - e2671 KW - biobanks KW - biological-effects KW - biological-structures KW - biological-substrates KW - combining KW - components KW - dbs KW - digital-libraries KW - extremal-biology KW - fdls KW - formal-biology KW - formal-digital-libraries KW - functionalities KW - genomes KW - homology KW - hyperefficiency KW - igem KW - kbs KW - libraries KW - model-organisms KW - modularity KW - modules KW - molecular-machines KW - molecular-structures KW - registries KW - repositories KW - reusability KW - sequences KW - synthetic-biology AU - Peccoud, Jean AU - Blauvelt, Megan AU - Cai, Yizhi AU - Cooper, Kristal AU - Crasta, Oswald AU - Delalla, Emily AU - Evans, Clive AU - Folkerts, Otto AU - Lyons, Blair AU - Mane, Shrinivasrao AU - Shelton, Rebecca AU - Sweede, Matthew AU - Waldon, Sally PY - 2008/07/16/ UR - http://dx.doi.org/10.1371/journal.pone.0002671 ER -