title: Targeted development of registries of biological parts.
abstract: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America. peccoud@vt.edu
authors.forename: Jean
authors.initials: J
authors.lastname: Peccoud
authors.forename: Megan F
authors.initials: MF
authors.lastname: Blauvelt
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Cai
authors.forename: Kristal L
authors.initials: KL
authors.lastname: Cooper
authors.forename: Oswald
authors.initials: O
authors.lastname: Crasta
authors.forename: Emily C
authors.initials: EC
authors.lastname: DeLalla
authors.forename: Clive
authors.initials: C
authors.lastname: Evans
authors.forename: Otto
authors.initials: O
authors.lastname: Folkerts
authors.forename: Blair M
authors.initials: BM
authors.lastname: Lyons
authors.forename: Shrinivasrao P
authors.initials: SP
authors.lastname: Mane
authors.forename: Rebecca
authors.initials: R
authors.lastname: Shelton
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Sweede
authors.forename: Sally A
authors.initials: SA
authors.lastname: Waldon
mesh_terms: D001695:Biology; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D015723:Gene Library; D005821:Genetic Techniques; D005822:Genetic Vectors; D007256:Information Systems; D008954:Models, Biological; D010957:Plasmids / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D049490:Systems Biology; D013696:Temperature
chemical_list: D004247:DNA