TY - JOUR
T1 - A standard-enabled workflow for synthetic biology
AU - Myers, Chris J.
AU - Beal, Jacob
AU - Gorochowski, Thomas E.
AU - Kuwahara, Hiroyuki
AU - Madsen, Curtis
AU - McLaughlin, James Alastair
AU - Misirli, Göksel
AU - Nguyen, Tramy
AU - Oberortner, Ernst
AU - Samineni, Meher
AU - Wipat, Anil
AU - Zhang, Michael
AU - Zundel, Zach
N1 - Publisher Copyright:
© 2017 The Author(s).
PY - 2017/6/15
Y1 - 2017/6/15
N2 - A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.
AB - A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.
UR - http://www.scopus.com/inward/record.url?scp=85020877918&partnerID=8YFLogxK
U2 - 10.1042/BST20160347
DO - 10.1042/BST20160347
M3 - Review article
C2 - 28620041
AN - SCOPUS:85020877918
SN - 0300-5127
VL - 45
SP - 793
EP - 803
JO - Biochemical Society Transactions
JF - Biochemical Society Transactions
IS - 3
ER -