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![Page 1: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi-cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader035.fdocuments.in/reader035/viewer/2022062311/5a4d1b3d7f8b9ab05999f450/html5/thumbnails/1.jpg)
Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi-cation of Synthetic Biology DesignsJacob Beal, Bryan Bartley, Kevin Clancy, Goksel Misirli, Nicholas Roehner (Editors), Herbert Sauro (Chair), & SBOL community
SEED ConferenceBoston, MAJune, 2015
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The SBOL Community
• 100+ people from all around the world• 30 universities, 14 companies, 8 others• Ongoing development starting 2008
Majorfunders:
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Synthetic Biology Open Language (SBOL)
FASTA
GenBank
SBOL 1.1
SBOL 2.0
ACTGTGCCGTTAAACGTGATTAAATCCGTACTGATAT…
TetR GFPpTet
aTcGFP
aTc detector GFP reporter
TetR GFPpTet
aTc detector GFP reporter
TetR GFPpTet
TetR
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Purpose of SBOL
• lots of ways of describing parts of systems• SBOL glues them all together into a unified
system
• Diagram:– sequences, BioPAX, SO, CHEBI, SBO, models, data
sheets on edges– SBOL appears as a link in the center
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Components of SBOL
SBOLv Glyphs
Tool
Tool
Tool
Tool
Tool
SBOL 2.0Data Model
Developer Community
fonts
examples
serialization
ontologies
images
libSBOL
SBOLdocuments
SBOLdocuments
SBOLdocuments
Other standards& repositories
GenBank
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What SBOL 2.0 Represents
• Sequence structure• Incomplete designs• Qualitative function
TetRpTet
aTc detector aTc
TetR
GFP
GFP
GFP reporter
• Heterarchical composition• Links to other information
GenBankMeasurement Data
Strain Information
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Simple Integration with non-SBOL Data
TetR GFPpTet
aTcGFP
aTc detector GFP reporter
TetR
Strain Information
• Embed SBOL in data• Embed data in SBOL
• Link SBOL to data• Links data to SBOL
Whatever model works best for the tools…
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SBOL supports many workflows
UserRepositories
Automation Vendors
User
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SBOL supports many workflows
• Reuse/ShareUser
Repositories
Automation Vendors
User
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SBOL supports many workflows
UserRepositories
Automation Vendors
User• Reuse/Share• Visualize
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SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model
UserRepositories
Automation Vendors
User
![Page 12: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi-cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader035.fdocuments.in/reader035/viewer/2022062311/5a4d1b3d7f8b9ab05999f450/html5/thumbnails/12.jpg)
SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model• Synthesize/Build
UserRepositories
Automation Vendors
User
![Page 13: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi-cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader035.fdocuments.in/reader035/viewer/2022062311/5a4d1b3d7f8b9ab05999f450/html5/thumbnails/13.jpg)
SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model• Synthesize/Build• Automate
UserRepositories
Automation Vendors
User
![Page 14: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi-cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader035.fdocuments.in/reader035/viewer/2022062311/5a4d1b3d7f8b9ab05999f450/html5/thumbnails/14.jpg)
Workflow: Reuse & Share
SBOLhub• Searchable repository for
public, private designs• Journal integration for
"one-click" private review
• Import SBOL/FASTA/GenBank, Export SBOL
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Workflow: Reuse & Share
ICE• Web of integrated public and
private design registries• Sequences, plasmids,
strains, visualization• SBOL, Genbank, FASTA
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Workflow: Visualize
Pigeon• Input simple network
description language• Design visualization
using SBOL glyphs
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Workflow: Design & Model
iBioSim• Graphical design of
reaction networks• Import or export both
SBML and SBOL 2.0• Simulate ODE, SSA
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Workflow: Design & Model
TinkerCell• Modular graphical
design of GRNs• SBOL import/expert• Simulate ODE, SSA
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Workflow: Design & Model
BioCompiler• Generate GRN design
from functional program• SBOL visualization and
design output• ODE simulations
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Workflow: Design & Model
Cello• Generate repressor
design from logic spec• SBOL encodes gate
library and outputs• Used w. TetR homologs
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Workflow: Synthesize/Build
waiting for picture/movie from kevin
VectorNTI• SBOL import/export• features to
highlight?
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j5• Import SBOL designs• Generate assembly
plans, oligos, protocols• Support for onward
laboratory automation
Workflow: Automate
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Call to Action
• Tool builders, use SBOL• Laboratory practitioners, come
talk about what tools you need• note about IWBDA
http://sbolstandard.org/