synthetic biology open language (sbol): community-driven standard for communi-cation of synthetic...
DESCRIPTION
The SBOL Community Major funders: Community has: more than 100 people, representing 30 universities, 14 companies, 8 other institutions 100+ people from all around the world 30 universities, 14 companies, 8 others Ongoing development starting 2008 Major funders:TRANSCRIPT
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
The SBOL Community
• 100+ people from all around the world• 30 universities, 14 companies, 8 others• Ongoing development starting 2008
Majorfunders:
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
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
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
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
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…
SBOL supports many workflows
UserRepositories
Automation Vendors
User
SBOL supports many workflows
• Reuse/ShareUser
Repositories
Automation Vendors
User
SBOL supports many workflows
UserRepositories
Automation Vendors
User• Reuse/Share• Visualize
SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model
UserRepositories
Automation Vendors
User
SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model• Synthesize/Build
UserRepositories
Automation Vendors
User
SBOL supports many workflows
• Reuse/Share• Visualize• Design/Model• Synthesize/Build• Automate
UserRepositories
Automation Vendors
User
Workflow: Reuse & Share
SBOLhub• Searchable repository for
public, private designs• Journal integration for
"one-click" private review
• Import SBOL/FASTA/GenBank, Export SBOL
Workflow: Reuse & Share
ICE• Web of integrated public and
private design registries• Sequences, plasmids,
strains, visualization• SBOL, Genbank, FASTA
Workflow: Visualize
Pigeon• Input simple network
description language• Design visualization
using SBOL glyphs
Workflow: Design & Model
iBioSim• Graphical design of
reaction networks• Import or export both
SBML and SBOL 2.0• Simulate ODE, SSA
Workflow: Design & Model
TinkerCell• Modular graphical
design of GRNs• SBOL import/expert• Simulate ODE, SSA
Workflow: Design & Model
BioCompiler• Generate GRN design
from functional program• SBOL visualization and
design output• ODE simulations
Workflow: Design & Model
Cello• Generate repressor
design from logic spec• SBOL encodes gate
library and outputs• Used w. TetR homologs
Workflow: Synthesize/Build
waiting for picture/movie from kevin
VectorNTI• SBOL import/export• features to
highlight?
j5• Import SBOL designs• Generate assembly
plans, oligos, protocols• Support for onward
laboratory automation
Workflow: Automate
Call to Action
• Tool builders, use SBOL• Laboratory practitioners, come
talk about what tools you need• note about IWBDA
http://sbolstandard.org/