synthetic biology open language (sbol): community-driven standard for communi-cation of synthetic...

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

Resources for Users / Developers

http://sbolstandard.org/

Call to Action

• Tool builders, use SBOL• Laboratory practitioners, come

talk about what tools you need• note about IWBDA

http://sbolstandard.org/