PMID- 27110633
OWN - NLM
STAT- MEDLINE
DCOM- 20170306
LR  - 20170306
IS  - 2161-5063 (Electronic)
IS  - 2161-5063 (Linking)
VI  - 5
IP  - 6
DP  - 2016 Jun 17
TI  - Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems.
PG  - 507-17
LID - 10.1021/acssynbio.5b00232 [doi]
AB  - Recently, semirational approaches that rely on combinatorial assembly of 
      characterized DNA components have been used to engineer biosynthetic pathways. In 
      practice, however, it is not practical to assemble and test millions of pathway 
      variants in order to elucidate how different DNA components affect the behavior 
      of a pathway. To address this challenge, we apply a rigorous mathematical 
      approach known as design of experiments (DOE) that can be used to construct 
      empirical models of system behavior without testing all variants. To support this 
      approach, we have developed a tool named Double Dutch, which uses a formal 
      grammar and heuristic algorithms to automate the process of DOE library design. 
      Compared to designing by hand, Double Dutch enables users to more efficiently and 
      scalably design libraries of pathway variants that can be used in a DOE framework 
      and uniquely provides a means to flexibly balance design considerations of 
      statistical analysis, construction cost, and risk of homologous recombination, 
      thereby demonstrating the utility of automating decision making when faced with 
      complex design trade-offs.
FAU - Roehner, Nicholas
AU  - Roehner N
AD  - Department of Electrical and Computer Engineering, Boston University , Boston, 
      Massachusetts 02215, United States.
FAU - Young, Eric M
AU  - Young EM
AD  - Department of Biological Engineering, Massachusetts Institute of Technology , 
      Cambridge, Massachusetts 02139, United States.
FAU - Voigt, Christopher A
AU  - Voigt CA
AD  - Department of Biological Engineering, Massachusetts Institute of Technology , 
      Cambridge, Massachusetts 02139, United States.
FAU - Gordon, D Benjamin
AU  - Gordon DB
AD  - Department of Biological Engineering, Massachusetts Institute of Technology , 
      Cambridge, Massachusetts 02139, United States.
FAU - Densmore, Douglas
AU  - Densmore D
AD  - Department of Electrical and Computer Engineering, Boston University , Boston, 
      Massachusetts 02215, United States.
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20160503
PL  - United States
TA  - ACS Synth Biol
JT  - ACS synthetic biology
JID - 101575075
SB  - IM
MH  - *Algorithms
MH  - Biosynthetic Pathways
MH  - Gene Library
MH  - *Software
MH  - Synthetic Biology/*methods
MH  - Workflow
EDAT- 2016/04/26 06:00
MHDA- 2017/03/07 06:00
CRDT- 2016/04/26 06:00
PHST- 2016/04/26 06:00 [entrez]
PHST- 2016/04/26 06:00 [pubmed]
PHST- 2017/03/07 06:00 [medline]
AID - 10.1021/acssynbio.5b00232 [doi]
PST - ppublish
SO  - ACS Synth Biol. 2016 Jun 17;5(6):507-17. doi: 10.1021/acssynbio.5b00232. Epub 
      2016 May 3.