Sharing Structure and Function in Biological Design with SBOL 2.0.
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.
Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
Nicholas
N
Roehner
Raytheon BBN Technologies , Cambridge, Massachusetts 02138, United States.
Jacob
J
Beal
Thermo Fisher Scientific , Carlsbad, California 92008, United States.
Kevin
K
Clancy
Department of Bioengineering, University of Washington , Seattle, Washington 98195, United States.
Bryan
B
Bartley
School of Computing Science, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K.
Goksel
G
Misirli
Institute for Research in Immunology and Cancer, University of Montreal , Montreal, Quebec H3T 1J4, Canada.
Raik
R
Grünberg
U.S. Department of Energy Joint Genome Institute , Walnut Creek, California 94598, United States.
Ernst
E
Oberortner
Turing Ate My Hamster, Ltd. , Newcastle upon Tyne NE27 0RT, U.K.
Matthew
M
Pocock
Amyris, Inc. , Emeryville, California 94608, United States.
Michael
M
Bissell
School of Computing Science, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K.
Curtis
C
Madsen
Department of Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, United States.
Tramy
T
Nguyen
Department of Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, United States.
Michael
M
Zhang
Department of Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, United States.
Zhen
Z
Zhang
Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States.
Zach
Z
Zundel
Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
Douglas
D
Densmore
Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, Washington 98195, United States.
John H
JH
Gennari
School of Computing Science, Newcastle University , Newcastle upon Tyne NE1 7RU, U.K.
Anil
A
Wipat
Department of Bioengineering, University of Washington , Seattle, Washington 98195, United States.
Herbert M
HM
Sauro
Department of Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, United States.
Chris J
CJ
Myers
D004247:DNA; D053263:Gene Regulatory Networks; D011381:Programming Languages; D012313:RNA; D012984:Software; D058615:Synthetic Biology / Q000592:standards; D057188:Workflow
D012313:RNA; D004247:DNA