high%levelbiodesignautoma5on* · dnapartssequence assemblyinstruc5ons cells high level...

High-‐Level BioDesign Automa5on

Jacob Beal

SemiSynBio February, 2013

Overview

Is biology too hard for abstraction? High-Level BDA is possible now!

•  Tool-chains for BDA •  Compiling from HLL to biological circuits •  Building computational device libraries

Vision: WYSIWYG Synthetic Biology

Bioengineering should be like document preparation:

3

Why is this important?

•  Breaking the complexity barrier:

•  Multiplication of research impact •  Reduction of barriers to entry

*Sampling of systems in publica<ons with experimental circuits

207

2,100 2,700

7,500 14,600

32,000

583,000 1,080,000

100

1,000

10,000

100,000

1,000,000

1975 1980 1985 1990 1995 2000 2005 2010

Length in base pa

irs

Year

DNA synthesis Circuit size ?

4

[Purnick & Weiss, ‘09]

Why a tool-chain?

Organism Level Descrip5on

Cells

This gap is too big to cross with a single method!

5

The TASBE tool-chain architecture:


Abstract Gene5c Regulatory Network

DNA Parts Sequence

Assembly Instruc5ons

Cells

High level simulator

Coarse chemical simulator

Testing

High Level Descrip5on If detect explosives: emit signal If signal > threshold: glow red

Detailed chemical simulator

Modular architecture also open for flexible choice of organisms, protocols, methods, …

6

Ron Weiss

Douglas Densmore

Collaborators:

A Tool-Chain Example

(def simple-sensor-actuator ()! (let ((x (test-sensor)))! (debug x)! (debug-2 (not x))))!

If detect explosives: emit signal If signal > threshold: glow red

Mammalian Target E. coli Target



blue

[expr]

Dox

not

yellow

!"##$%&'(

!"##$%&'(

!"##$%&'(

!"##$%&'(


green

[expr]

Ara

not

red

!"##$%&'(

!"##$%&'(

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!"##$%&'(



!"#$

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*+,-) *+,-) *+,-)




!"#$%

&'(%

)*+,% !-#$.%

Transcription Factors

Promoters

)*+,%&'(%

Small Molecules

$/%

0% $.%

$1%

!"#$%

%!-#$.%


Promoters

234'%256%

Small Molecules

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9:% ;9:%

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)*+,%&'(% ;+)4%

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;?4@/,% ?4@/,B6,AC/CDE%;+)4%

!"#$%

&'(%

)*+,% !-#$.% 6,A:%

GRN AGRN

Feature Database Canonical AGRN

GRN

!"#$

%&'$

%&'($ )"#$

AGRN


Promoters

%&'($%&'$

Small Molecules

#*$

+$ #,$

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Promoters

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Feature Database Canonical AGRN




pC araC

pBad TetR GFP

araC TetR GFP RFPpTetpBad

Ara

pC

pTet

RFP




Uninduced Uninduced

Induced Induced

Focus: BioCompiler


Abstract Gene5c Regulatory Network

DNA Parts Sequence

Assembly Instruc5ons

Cells

High level simulator

Coarse chemical simulator

Testing

High Level Descrip5on If detect explosives: emit signal If signal > threshold: glow red

Detailed chemical simulator

Compila5on & Op5miza5on

13

Other tools aiming at high-‐level design: Cello, Eugene, GEC, GenoCAD, etc.

Transcriptional Logic Computations

14

  Operators translated to motifs:

IPTG not green

LacI

A IPTG

B

GFP outputs outputs outputs arg0 arg0

LacI A

IPTG

B GFP

Motif-Based Compilation

15

(def sr-latch (s r) (letfed+ ((o boolean (not (or r o-bar))) (o-bar boolean (not (or s o)))) o))

(green (sr-latch (aTc) (IPTG)))

Design Optimization

LacI B

IPTG

I

G

I F

GFP

D E1 E2

A

aTc J

H C

J TetR

UnopEmized: 15 funcEonal units, 13 transcripEon factors 16

GFP

Design Optimization

LacI F

IPTG

TetR

H

aTc

F

Final Op>mized: 5 func>onal units 4 transcrip>on factors

(def sr-latch (s r) (letfed+ ((o boolean (not (or r o-bar))) (o-bar boolean (not (or s o)))) o))

(green (sr-latch (aTc) (IPTG)))

UnopEmized: 15 funcEonal units, 13 transcripEon factors

H

17

Automated Synthesis of Complex Designs

Example: 4-bit adder Example: 4-bit counter

Alfa1

Uppermost

Mike1

AmCyan

Barber

Homework1

Bravo1

Lipstick

Mike1

Bribe

Nuisance Paw

Charlie1

Modesty

Grammar

Companionship

Woolen Hinder

Cultivation

Hinder

Delta1

Rubbish

Grammar

Dox

rtTA

EBFP2

EYFP

Echo1

Homecoming

Ripen

Feast

Nuisance Tidy

Foxtrot1

Liar

Ripen

GFP

Golf1

Feast

Tidy

Grammar

Yankee1

Handwriting

mKate

Hinder

EYFP

Homecoming

Barber

Homework1

Mend

Hotel1

Stocking

IND4

IND4I

Delta1

IND5

IND5I

Echo1

IND6

IND6I

Foxtrot1

IND7

IND7I

Old

IND8

IND8I

Hotel1

IPTG

LacI

India1

Companionship

Jealous

Barber Handwriting

Jealousy

Handwriting

Charlie1

Liar

Lipstick

India1

Mend

Paw

Mike1

Punctual

Modesty

Woolen

Nuisance

GFP

Paw

AmCyan

Punctual

EBFP2

RSL

RheoAct_Rec

Redden1

Jealous

Bravo1

Ripen

Redden1

Rubbish

Stocking

Tidy

Widower1

Uppermost

Victor1

Jealousy

Widower1

Bribe

Woolen

Victor1

Yankee1

Cultivation

mKate

Alfa1

rtTA IND8I IND7I IND6I IND5I IND4I LacI RheoAct_Rec

Golf1

AmCyan

Attentive

Sow Whichever

Avoidance

Grammar

Basin

Rotten Breadth

Bicycle

Obedient

Breadth

Bribe

Nuisance

Charlie1

Juliet Homemade

Cheat

Mat

Companionship

Deceive

Congratulate

Basin

Correction

Lengthen

Coward

Congratulate

Deceit1

WoolenCompanionship

Avoidance

Ink

Deceive

Descendant

Descendant

Disappearance

Woolen Spoon

Dox

rtTA

EBFP2

EYFP

Feast

Mend

Golf

Liar

Grammar

EBFP2 Parcel1

Homecoming

Jealous

Inclusive

Homemade

Golf Slippery

Homework

Whiskey1 mKate

Inclusive

Ink

Jealous

Homecoming Sour

Juliet

Ripen

Lengthen

Liar

Lima

AmCyan Charlie1

Madden

Coward

Mat

Bicycle

Mend

Multiplication

Multiplication

Homework

Nuisance

Attentive

Oar

Bribe

Obedient

EYFP Sadden1

Parcel1

Rotten MaddenCompanionshipDisappearance

Paw

Ripen

Rotten

Cheat

Sadden1

Sow Oar Madden Weed

Slippery

Lima

Sour

Sow

Feast

Spoon

Weed

Whichever

Whiskey1

Golf Juliet Oar Paw

Woolen

Correction

mKate

Deceit1

rtTA

OpEmized compiler already outperforms human designers

Barriers & Emerging Solutions:

•  Barrier: Availability of High-Gain Devices –  Emerging Solution: combinatorial device libraries

based on TALs, ZFs, miRNAs

•  Barrier: Characterization of Devices –  Emerging solution: TASBE characterization method

•  Barrier: Predictability of Biological Circuits –  Emerging solution: EQuIP prediction method

TASBE Method: Calibrated, Precise Characterization

TAL14 TAL21

pCAG

Dox

T2A rtTA3 VP16Gal4 pTRE

EBFP2 pTRE

R1 pUAS-‐Rep1

EYFP pCAG mkate pCAG

Characterization High Quality Predictions

103 104 105 106 107 108104

105

106

107

108

109

IFP MEFL

OFP

MEF

L

Non Normalized Cascade TAL21 TAL14 Interpolated Prediction transfer curve

103 104 105 106 107 108104

105

106

107

108

109

IFP MEFL

OFP

MEF

L

Non Normalized Cascade LmrA TAL14 Interpolated Prediction transfer curve

LmrA TAL14 TAL21 TAL14

pCAG

Dox


EBFP2 pTRE

R1 pUAS-‐Rep1 pUAS-‐Rep2

EYFP R2 pCAG mkate pCAG

High Quality Cascade Predictions

103 104 105 106 107 108104

105

106

107

108

109

IFP MEFL

OFP

MEF

L

Non Normalized Cascade TAL21 TAL14 Interpolated transfer curve

103 104 105 106 107 108104

105

106

107

108

109

IFP MEFL

OFP

MEF

L

Non Normalized Cascade LmrA TAL14 Interpolated transfer curve

LmrA TAL14 TAL21 TAL14 Distribu5on + dynamics models good predic5ons

pCAG

Dox


EBFP2 pTRE

R1 pUAS-‐Rep1 pUAS-‐Rep2

EYFP R2 pCAG mkate pCAG

Summary

High-Level BDA is possible now! •  EDA tool-chain approach works for BDA •  Optimized biological circuits can be generated

automatically from high-level specifications •  Emerging solutions for key barriers: device

libraries, characterization, prediction

•  Many opportunities for EDA tool adaptation: –  Combinatorial device design –  Flexible protocol automation –  Device characterization –  Circuit optimization, verification, safety, debugging

.. and going from cells to processors…

Inference resources focused propor<onally on areas of interest

ASH volumetric region management [Pruteanu, Dulman & Langendoen, ‘10]

Proto global-‐to-‐local compila<on & manifold computa<on model

Distor<on of computa<on around temporary and permanent faults

Spa>al Compu>ng Process Management

Characterization & Design Tools Online

https://synbiotools.bbn.com/

Acknowledgements:

Aaron Adler Joseph Loyall Rick Schantz Fusun Yaman

Ron Weiss Jonathan Babb Noah Davidsohn Ting Lu

Douglas Densmore Evan Appleton Swapnil Bhatia Traci Haddock Chenkai Liu Viktor Vasilev

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high%level*biodesign*automa5on* · dnaparts*sequence* assembly*instruc5ons* cells high level...

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high%levelbiodesignautoma5on* · dnapartssequence assemblyinstruc5ons cells high level...