The LASER database: Formalizing design rules for metabolic engineering
The ability of metabolic engineers to conceptualize, implement, and evaluate strain designs has dramatically increased in the last decade. Unlike other engineering fields, no centralized, open-access, and easily searched repository exists for cataloging these designs and the lessons learned from the...
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doaj-9a31ee6f051c4d94a09b58349bb090762020-11-24T20:54:50ZengElsevierMetabolic Engineering Communications2214-03012015-12-0123038The LASER database: Formalizing design rules for metabolic engineeringJames D. Winkler0Andrea L. Halweg-Edwards1Ryan T. Gill2Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USADepartment of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USACorresponding author.; Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USAThe ability of metabolic engineers to conceptualize, implement, and evaluate strain designs has dramatically increased in the last decade. Unlike other engineering fields, no centralized, open-access, and easily searched repository exists for cataloging these designs and the lessons learned from their construction and evaluation. To address this issue, we have developed a repository for metabolic engineering strain designs, known as LASER (Learning Assisted Strain EngineeRing, laser.colorado.edu) and a formal standard for disseminating designs to metabolic engineers. Curation of every available genetically-defined E. coli and S. cerevisiae strain from 310 metabolic engineering papers published over the last 21 years yields a total of 417 designs containing a total of 2661 genetic modifications. This collection has been deposited in LASER and represents the known bibliome of genetically defined and tested metabolic engineering designs in the academic literature. Properties of LASER designs and the analysis pipeline are examined to provide insight into LASER capabilities. Several future research directions utilizing LASER capabilities are discussed to highlight the potential of the LASER database for metabolic engineering. Keywords: Metabolic engineering, Synthetic biology, Standardization, Design toolshttp://www.sciencedirect.com/science/article/pii/S2214030115300031 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
James D. Winkler Andrea L. Halweg-Edwards Ryan T. Gill |
spellingShingle |
James D. Winkler Andrea L. Halweg-Edwards Ryan T. Gill The LASER database: Formalizing design rules for metabolic engineering Metabolic Engineering Communications |
author_facet |
James D. Winkler Andrea L. Halweg-Edwards Ryan T. Gill |
author_sort |
James D. Winkler |
title |
The LASER database: Formalizing design rules for metabolic engineering |
title_short |
The LASER database: Formalizing design rules for metabolic engineering |
title_full |
The LASER database: Formalizing design rules for metabolic engineering |
title_fullStr |
The LASER database: Formalizing design rules for metabolic engineering |
title_full_unstemmed |
The LASER database: Formalizing design rules for metabolic engineering |
title_sort |
laser database: formalizing design rules for metabolic engineering |
publisher |
Elsevier |
series |
Metabolic Engineering Communications |
issn |
2214-0301 |
publishDate |
2015-12-01 |
description |
The ability of metabolic engineers to conceptualize, implement, and evaluate strain designs has dramatically increased in the last decade. Unlike other engineering fields, no centralized, open-access, and easily searched repository exists for cataloging these designs and the lessons learned from their construction and evaluation. To address this issue, we have developed a repository for metabolic engineering strain designs, known as LASER (Learning Assisted Strain EngineeRing, laser.colorado.edu) and a formal standard for disseminating designs to metabolic engineers. Curation of every available genetically-defined E. coli and S. cerevisiae strain from 310 metabolic engineering papers published over the last 21 years yields a total of 417 designs containing a total of 2661 genetic modifications. This collection has been deposited in LASER and represents the known bibliome of genetically defined and tested metabolic engineering designs in the academic literature. Properties of LASER designs and the analysis pipeline are examined to provide insight into LASER capabilities. Several future research directions utilizing LASER capabilities are discussed to highlight the potential of the LASER database for metabolic engineering. Keywords: Metabolic engineering, Synthetic biology, Standardization, Design tools |
url |
http://www.sciencedirect.com/science/article/pii/S2214030115300031 |
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