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Transcript of Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic...
![Page 1: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/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
![Page 2: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/html5/thumbnails/2.jpg)
The SBOL Community
• 100+ people from all around the world• 30 universities, 14 companies, 8 others• Ongoing development starting 2008
Majorfunders:
![Page 3: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/html5/thumbnails/3.jpg)
Synthetic Biology Open Language
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 2.0
Lots of different synthetic biology resources…
GenBank
Measurement Data
Strain Data
LIMSLab Automation
HT Assays
Repositories & Databases Automation & Integration
Modeling
Sequencing & Synthesis
Emerging Approaches
some icons
… SBOL is a "hub" for linking them togetherBioPAX BioModels.Net
SOChEBI
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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& resources
GenBank
![Page 6: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/html5/thumbnails/6.jpg)
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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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/Share
UserRepositories
Automation Vendors
User
![Page 10: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/html5/thumbnails/10.jpg)
SBOL supports many workflows
UserRepositories
Automation Vendors
User
• Reuse/Share• Visualize
![Page 11: Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communi- cation of Synthetic Biology Designs Jacob Beal, Bryan Bartley, Kevin Clancy,](https://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/html5/thumbnails/11.jpg)
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://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/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://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/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://reader034.fdocuments.in/reader034/viewer/2022042822/56649f305503460f94c4afce/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
http://pigeoncad.org/
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Workflow: Design & Model
iBioSim• Graphical design of
reaction networks• Import or export both
SBML and SBOL 2.0• Simulate ODE, SSAwww.async.ece.utah.edu/iBioSim/
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Workflow: Design & Model
TinkerCell• Modular graphical
design of GRNs• SBOL import/export• Simulate ODE, SSA
http://www.tinkercell.com/
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Workflow: Design & Model
BioCompiler• Generate GRN design
from functional program• SBOL visualization and
design output• ODE simulationshttps://synbiotools.bbn.com/
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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
http://www.teselagen.com
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Call to Action!
• Tool builders, use SBOL• Laboratory practitioners, come
talk about what tools you need• NIST S.B. Standards Consortium
– Digital Biological Information WG
• Community meeting at IWBDA– August 19-21, Seattle
http://sbolstandard.org/