Proto BioCompiler Jacob Beal October, 2011 Work partially sponsored by DARPA; the views and...

Proto BioCompiler

Jacob Beal

October, 2011

Work partially sponsored by DARPA; the views and conclusions contained in this document are those of the authors and not DARPA or the U.S. Government. 1

Vision: WYSIWYG Synthetic Biology

Bioengineering should be like document preparation:

2

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 publications with experimental circuits

1975 1980 1985 1990 1995 2000 2005 2010100

1,000

10,000

100,000

1,000,000

207

2,100 2,700

7,500 14,600

32,000

583,0001,080,000

Year

Leng

th in

bas

e pa

irs

DNA synthesis Circuit size ?

4

Why a tool-chain?

Organism Level Description

Cells

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

5

The TASBE architecture:

Organism Level Description

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

Cells

High level simulator

Coarse chemical simulator

Testing

High Level DescriptionIf detect explosives: emit signalIf signal > threshold: glow red

Detailed chemical simulator

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

6

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

7

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

8

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

rtTA CFP B EYFP

Dox

9

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

rtTA CFP B EYFP

Dox

pHef1a rtTA pTre CFP pTre LacI pHef1a-LacO1Oid

EYFPmirff4 4xff4

10

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

rtTA CFP B EYFP

Dox

pHef1a rtTA pTre CFP pTre LacI pHef1a-LacO1Oid

EYFPmirff4 4xff4

11

A Tool-Chain Example

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

rtTA CFP B EYFP

Dox

pHef1a rtTA pTre CFP pTre LacI pHef1a-LacO1Oid

EYFPmirff4 4xff4

12

Today’s focus: BioCompiler

Organism Level Description

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

Cells

High level simulator

Coarse chemical simulator

Testing

High Level DescriptionIf detect explosives: emit signalIf signal > threshold: glow red

Detailed chemical simulator

Compilation &Optimization

13

Transcriptional Logic

14

Motif-Based Compilation

• High-level primitives map to GRN design motifs– e.g. logical operators:

(primitive not (boolean) boolean :grn-motif ((P high R- arg0 value T)))

arg0 value

15

High-level primitives map to GRN design motifs e.g. logical operators, actuators:

(primitive green (boolean) boolean :side-effect :type-constraints ((= value arg0)) :grn-motif ((P R+ arg0 GFP|arg0 value T)))

GFP valuearg0

Motif-Based Compilation

16

High-level primitives map to GRN design motifs e.g. logical operators, actuators, sensors:

(primitive IPTG () boolean :grn-motif ((P high LacI|boolean T) (RXN (IPTG|boolean) represses LacI) (P high R- LacI value T)))

valueLacI

IPTG

Motif-Based Compilation

17

Functional program gives dataflow computation:

(green (not (IPTG)))

Motif-Based Compilation

18

Functional program gives dataflow computation:

(green (not (IPTG)))

IPTG not green

Motif-Based Compilation

19

Operators translated to motifs:

IPTG not green

Motif-Based Compilation

20

Operators translated to motifs:

IPTG not green

LacI

AIPTG

B

GFPoutputs outputs outputsarg0arg0

Motif-Based Compilation

21

Operators translated to motifs:

IPTG not green

LacI A

IPTG

B GFP

LacI

AIPTG

B

GFPoutputs outputs outputsarg0arg0

Motif-Based Compilation

22

LacI A

IPTG

B GFP

Optimization

23

LacI A

IPTG

B GFP

LacI A

IPTG

B GFP

Copy Propagation

Optimization

24

LacI A

IPTG

B GFP

LacI A

IPTG

B GFP

Copy Propagation

LacI A

IPTG

GFP

Dead Code Elimination

Optimization

25

LacI A

IPTG

B GFP

LacI A

IPTG

B GFP

Copy Propagation

LacI A

IPTG

GFP

Dead Code Elimination

LacI A

IPTG

GFP

Dead Code Elimination

Optimization

26

(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)))

Complex System: Feedback Latch

27

(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)))

Complex System: Feedback Latch

LacI B

IPTG

I

G

IF

GFP

DE1 E2

A

aTcJ

HC

JTetR

Unoptimized: 15 functional units, 13 transcription factors 28

(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)))

Optimization of Complex Designs

LacI B

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

G

IF

GFP

DE1 E2

A

aTcJ

HC

JTetRCopy Propagation29

E1

(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)))

Optimization of Complex Designs

LacI

B

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

G

IF

GFP

D

A

aTcJ

HC

J

TetR

Common Subexp. Elim.30

E1

(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)))

Optimization of Complex Designs

LacI

B

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

G

IF

GFP

D

A

aTcH JC

J

TetR

NOR CompressionH

31

E1

(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)))

Optimization of Complex Designs

LacI

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

G

IF

GFP

aTcH

TetR

Dead Code EliminationH

32

E1

(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)))

Optimization of Complex Designs

LacI

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

G

IF

GFP

aTcH

TetR

Copy PropagationH

33

HE1

(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)))

Optimization of Complex Designs

LacI

IPTG

Unoptimized: 15 functional units, 13 transcription factors

IG

IF

GFP

aTc

TetR

Common Subexp. Elim.H

34

H

(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)))

Optimization of Complex Designs

LacI

IPTG

Unoptimized: 15 functional units, 13 transcription factors

I

IF

GFP

aTc

TetR

Dead Code EliminationH

35

H

(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)))

Optimization of Complex Designs

Unoptimized: 15 functional units, 13 transcription factors

I F GFP

H

LacI

IPTG

TetRaTc

I

36

H

(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)))

Optimization of Complex Designs

Unoptimized: 15 functional units, 13 transcription factors

F GFP

H

LacI

IPTG

TetRaTc

F

NOR Compression

I

I

37

H

(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)))

Optimization of Complex Designs

Unoptimized: 15 functional units, 13 transcription factors

F GFP

H

LacI

IPTG

TetRaTc

F

Dead Code Elimination38

GFP

Optimization of Complex Designs

LacIF

IPTG

TetR

H

aTc

F

Final Optimized:5 functional units4 transcription 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)))

Unoptimized: 15 functional units, 13 transcription factors

H

39

Compilation & Optimization Results:

• Automated GRN design for arbitrary boolean logic and feedback systems– Verification in ODE simulation

• Optimization competitive with human experts:– Test systems have 25% to 71% complexity reduction– Optimized systems are often homologous with hand

designed networks

40

pHef1a rtTA EYFPHef1a-LacO1OidmKate Tre pLac

Dox

EBFPTre

Realization with Characterized DNA parts

pHef1a

41

Onward Through the Tool-Chain…

(yellow (not (cyan (Dox))))

High level simulator

Coarse chemical simulator

Detailed chemical simulator

Testing

Cells

Abstract Genetic Regulatory Network

DNA Parts Sequence

Assembly Instructions

High Level Description

If detect explosives:emit signal

If signal > threshold:glow red

Organism Level Description

Dox cyan not yellow

rtTA CFP B EYFP

Dox

pHef1a rtTA pTre CFP pTre LacI pHef1a-LacO1Oid

EYFPmirff4 4xff4

42

Proto is available

http://proto.bbn.com/

(or google “MIT Proto”)

• Includes libraries, compiler, kernel, simulator, platforms• Licensed under GPL (w. libc-type exception)

BioCompiler is available on request

43

TASBE Project Team:

Jacob Beal (PI)

Aaron Adler

Rick Schantz

Fusun Yaman

Joseph Loyall (PMs)

Ron Weiss (co-PI)

Jonathan Babb

Noah Davidsohn

Douglas Densmore (co-PI)

Swapnil Bhatia

Traci Haddock

Viktor Vasilev

Chenkai Liu

Sponsored by:44