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Emerging Standards in Synthetic Biology

Herbert M SauroMichal Galdzicki and Deepak ChandranUniversity of Washington, Seattle

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SBML in a NutshellBottom-Up Effort

• A machine-readable format for representing computational models in systems biology

• Domain: systems of biochemical reactions• Specified using XML• Components in SBML reflect the natural

conceptual constructs of the domain• Now over 200 tools use SBML

www.sbml.orgFunding

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SBML Ecosystem SBML

Databases

Unambiguous Model

Exchange

Semantic Annotations

Simulator Comparison and

ComplianceJournals

Diagrams

SEDML: Simulation Experiment Description LanguageSBGN : Systems Biology Graphical Notation

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What is Synthetic Biology

Synthetic Biology is the “design and construction of novel artificial biological pathways, organismsor devices, or the redesign of existing natural biological systems.” (Royal Society)

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10 years of Synthetic Biology

Gardner TS, et al. Construction of a genetic toggle switch in Escherichia coli. Nature 2000; 403: 339-342.

Elowitz and Leibler; A Synthetic Oscillatory Network ofTranscriptional Regulators Nature. 2000; 403: 335-8.

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Synthetic Biology Workflow

“Creating cells that are able to excrete insulin at a specified rate during their optimal growth.”

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Overall Aim of the Standardization Effort

To support the synthetic biology workflow:

1. Laboratory parts management2. Simulation/Analysis3. Design4. Assembly5. Repositories - preferably distributed

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The Immediate NeedTake any current publication on a synthetic circuit and try to reproduce it, let me know how you get on.

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Long-term Aim of the Standardization Effort

Specifically:

• To allow researches to electronically exchange designs with round-tripping.

• To sent designs to bio-fabrication centers for assembly.

• To allow storage of designs in repositories and for publication purposes.

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Synthetic Biology Open Language: SBOL

http://www.sbolstandard.org/

1.SBOL Semantic*2.SBOL Visual*3.SBOL Script

First meeting in 2008, Seattle, fundedby Microsoft

Synthetic Biology Data Exchange GroupSynthetic Biology Open Language (SBOL)

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SBOL-visualSBOL-semantic

iBioSim

http://www.sbolstandard.org/

UK, Imperial College

EU 7th Framework Programme

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SBOL Visual (SBOLv)

Developed at the BerkeleyBIOFAB (Endy and Arkin) • Current about 40 symbols• Used to visually annotate‘features’ on a DNA

Three symbol groups at present:

1. Central Dogma2. Genetic Engineering3. Devices

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SBOL Visual (Implemented in Spectacles and TinkerCell)

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SBOL: Reuse of biological parts

semantic

Sequence Annotation

1-80

Terminator

81-88

BioBrick Scar

BioBrick Scar

89-129

Terminator

B0010 B0012

Part

B0015

Create a common language for engineers to describe and send parts

Synthetic Biologist A

Synthetic Biologist B

Fabricate

Synthetic Biology Open Language (SBOL)

visual

DNA Components

Engineer

New genetic device

Michal Galdzicki describe and send

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Figure 1. Diagram of the SBOL Semantic structure, illustrated with a set of information about a synthetic biology construct. a. A simplified Class (black rectangles) hierarchy (black open faced arrows) describes types (colored open faced arrows )of Individual data elements (yellow rounded rectangles) and the composition relationships between them (closed faced arrows). The example can be read as: Sample (pink) SS002 contains UW002 cells (dark green) of the MG1655 E. coli strain, which contain a plasmid (purple) pUW4510, which is composed of an parts (dark blue) an insert B0015 and vector backbone pSB1A2. The pSB1A2 vector backbone complies with the Assembly Standard (light blue) BBF RFC 10. The B0015 sequence annotations (green) specify three features (orange), the BioBrick Scar, and the parts (blue and orange indicating multiple inheritance), B0010 and B0012, which serve as transcriptional termination signals. b. Data type Properties used to hold information for each SBOL class follow the colon.

Sequ

ence

Ann

otati

on

Vect

or B

ackb

one

Sample

CellPh

ysic

al D

NA

Assembly Standard

pSB1A2

BBF RFC 10

SS002

pUW4510

MG1655type type

typetype

type

cell

dna

insertvector

format

UW002strain

Sequence Feature

B0015

type

annotation

1-80

feature

Terminator

81-88

BioBrick Scarfeature

BioBrick Scar

89-129

feature

Terminator

annotation annotation

type type

subClassOf subClassOfsubClassOf

subC

lass

Of

B0010 B0012

Part

type

Plas

mid

subC

lass

Of

type

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Parts Registry at MIT

Database of parts, basically a wiki, objectmodel not documentedand was generally not available to the public until this year.

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SBOLr is a web front for a knowledge base of standard biological parts

http://sbolr.bhi.washington.edu/

JBEIr Software by Timothy Ham & Zinovii Dmytriv

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Software support: libSBOL

Michal Galdzicki

CAD Tool

TinkerCell

Sequence Editor

Parts KB

libSBOL

SBOL-semantic

Repository

Allow for ease of access to information by software tools, using Semantic Web standards.

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List of Software in the Working Group• Clotho (BU,Berkeley), Java

Connects users to repositories of biological parts. Plugin tools then define the various functions that can be performed, mainly related to lab and parts managements. Douglas Densmore

• GenoCAD (VT)Web based tool for the design of biological devices using an attribute grammar which defines the legal composition of parts. Jean Peccoud

• iBioSim (Utah), JavaAdvanced simulation and analysis tool for synthetic and systems biology. Chris Myers

• JBEI Repository (Java), DOE support infrastructure Timothy Ham & Zinovii Dmytriv

• SBOLr (Currently Python but moving to Java)Test parts repository, ~5000 parts Michal Galdzicki

• TinkerCell (UW), C++/QtExtensible visual design tool with support for modules, eg simulation, annotation. Deepak Chandran

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Current Status of Standard• First official release will be at Synthetic Biology 5.0 at

Stanford, June, 2011

• libSBOL 1.0 available at: http://github.com

• Import/Export: GenBank, RDF, JSON

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TinkerCell: Project to explore the potential of computer aided design in synthetic biology

First prototype called Athena Developed by Bergmann and Chandran fundedby Microsoft

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Layered Architecture: Based on C++/Qt

Octave,

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All Parts can be Semantically Annotated. This allow plug-ins to interpret a given design.

Enzyme

Transcription Factor

Enzyme catalysis

BindingTranslation

Reporter

Elongation

CodingPromoter Terminator

Transcription

mRNA

Currently there is noformal ontology forsynthetic biology but onewill need to be developed.

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A TinkerCell model can be composed of sub-models

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A TinkerCell model can be composed of sub-models

?

?

?

? ?

?

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Users can add new plugins using C++, C, Octave, or Python languages

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Availabilitywww.tinkercell.com (Windows, Mac and Linux, released under BSD)Contact author for details (dchandran1@gmail.com)

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SciPy• optimization• matrix operations• statistics• numerical methods• frequency analysis

NetworkX (lanl.gov)• graph analysis• graph layout

• structural analysis• sensitivity analysis• bifurcation analysis• parameter scan• simulation

lp_solve• flux balance analysis

Many C and Python packages are included with TinkerCell

Sundials• Time-course simulation• Steady state plot

Custom programs• Gillespie algorithm• Hill equation derivation• 2^N automatic binding events• Loops in Jacobian

AntimonySBML and CellML support

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Demo: Repressilator

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Acknowledgements: Collaborators and Funding

UWDeepak Chandran, Michal Galdziki, Sean Sleight, Bryan Bartley, Alex Neilson

BioFAB (Berkeley, Stanford)Cesar Rodriguez, Drew Endy , Chris Anderson

Virginia Tech JBEI (DOE) Jean Peccoud Timothy Ham & Zinovii Dmytriv

Boston University CRG, Spain Douglas Densmore Raik Grunberg

FundingNational Library of Medicine (Galdziki)Other funding from NIH (JSim/SBW) , NIH (SBW) and NSF (FIBR,Tinkercell), Microsoft Strategic Research, BioFAB (NSF), JBEI (DOE)

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Textbook:Enzyme Kinetics for Systems Biology

• Available as e-book or paperback on www.analogmachine.org & • 318 pages, 94 illustrations and 75 exercises• E-book - $9.95• Paperback - $29.95

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Sequence Refinement

Examples include avoiding specific restriction sites or optimizing the codon usage. The sequence might also be optimized to avoid repeated regions that may be prone to recombination or secondary structures.

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The SBOL semantic structure

Sequence Annotation

type

type

annotation

1-80

feature

Terminator

81-88

BioBrick Scar

feature

BioBrick Scar

89-129

feature

Terminator

annotation annotation

type type

B0010 B0012

Parttype

B0015

type = instance-of

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Each component in the TinkerCell diagram is associated with one or more tables