proto biocompiler jacob beal october, 2011 work partially sponsored by darpa; the views and...
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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
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Transcriptional Logic
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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
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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
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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
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Functional program gives dataflow computation:
(green (not (IPTG)))
Motif-Based Compilation
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Functional program gives dataflow computation:
(green (not (IPTG)))
IPTG not green
Motif-Based Compilation
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Operators translated to motifs:
IPTG not green
Motif-Based Compilation
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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
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LacI A
IPTG
B GFP
Optimization
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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
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(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
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(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