Toward the first data acquisition standard in synthetic biology
File(s)
Author(s)
Sainz de Murieta, I
Bultelle, M
Kitney, RI
Type
Journal Article
Abstract
This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.
Date Issued
2016-08-19
Date Acceptance
2016-02-07
Citation
ACS Synthetic Biology, 2016, 5 (8), pp.817-826
ISSN
2161-5063
Publisher
American Chemical Society
Start Page
817
End Page
826
Journal / Book Title
ACS Synthetic Biology
Volume
5
Issue
8
Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Synthetic Biology, © 2016 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acssynbio.5b00222
Sponsor
Engineering & Physical Science Research Council (E
Engineering & Physical Science Research Council (EPSRC)
Identifier
https://pubs.acs.org/doi/10.1021/acssynbio.5b00222
Grant Number
EP/J02175X/1
EP/L011573/1
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biochemistry & Molecular Biology
data acquisition
characterization
standard
biopart
synthetic biology
MARKUP LANGUAGE
GENE-EXPRESSION
COMMUNICATION-SYSTEMS
ESCHERICHIA-COLI
TOGGLE SWITCH
NETWORK
MODELS
CONSTRUCTION
DEVICES
DESIGN
biopart
characterization
data acquisition
standard
synthetic biology
Data Curation
Databases, Factual
Information Storage and Retrieval
Molecular Sequence Data
Software
Synthetic Biology
Software
Molecular Sequence Data
Information Storage and Retrieval
Databases, Factual
Synthetic Biology
Data Curation
0304 Medicinal and Biomolecular Chemistry
0601 Biochemistry and Cell Biology
0903 Biomedical Engineering
Publication Status
Published
Date Publish Online
2016-02-23