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:
DNA synthesis
1,080,000
583,000
1,000,000
Length in base pairs
Circuit size
?
100,000
32,000
7,500
10,000
2,100
14,600
2,700
1,000
207
100
1975
1985
1995
Year
2005
• Multiplication of research impact
• Reduction of barriers to entry
4
*Sampling of systems in publications with experimental circuits
Why a tool-chain?
Organism Level Description
This gap is too big
to cross with a
single method!
Cells
5
The TASBE architecture:
Organism Level Description
High level simulator
High Level Description
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical simulator
Abstract Genetic Regulatory Network
Detailed chemical simulator
DNA Parts Sequence
Assembly Instructions
Testing
Modular architecture
also open for flexible
choice of organisms,
protocols, methods, …
Cells
6
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
High level
simulator
High Level
Description
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
Abstract Genetic
Regulatory Network
Detailed chemical
simulator
DNA Parts
Sequence
Assembly
Instructions
Testing
Cells
7
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
High level
simulator
yellow
High Level
Description
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
Abstract Genetic
Regulatory Network
Detailed chemical
simulator
DNA Parts
Sequence
Assembly
Instructions
Testing
Cells
8
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
yellow
High Level
Description
Dox
rtTA
High level
simulator
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
CFP
B
EYFP
Abstract Genetic
Regulatory Network
Detailed chemical
simulator
DNA Parts
Sequence
Assembly
Instructions
Testing
Cells
9
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
High level
simulator
yellow
High Level
Description
Dox
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
rtTA
CFP
B
Abstract Genetic
Regulatory Network
EYFP
Detailed chemical
simulator
DNA Parts
Sequence
pHef1a
rtTA
pTre
CFP
pTre
LacI
mirff4 pHef1a- EYFP
LacO1Oid
4xff4
Assembly
Instructions
Testing
Cells
10
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
High level
simulator
yellow
High Level
Description
Dox
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
rtTA
CFP
B
Abstract Genetic
Regulatory Network
EYFP
Detailed chemical
simulator
DNA Parts
Sequence
pHef1a
rtTA
pTre
CFP
pTre
LacI
mirff4 pHef1a- EYFP
LacO1Oid
4xff4
Assembly
Instructions
Testing
Cells
11
A Tool-Chain Example
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
High level
simulator
yellow
High Level
Description
Dox
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
rtTA
CFP
B
Abstract Genetic
Regulatory Network
EYFP
Detailed chemical
simulator
DNA Parts
Sequence
pHef1a
rtTA
pTre
CFP
pTre
LacI
mirff4 pHef1a- EYFP
LacO1Oid
4xff4
Assembly
Instructions
Testing
Cells
12
Today’s focus: BioCompiler
Organism Level Description
High level simulator
Compilation
&
Optimization
High Level Description
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical simulator
Abstract Genetic Regulatory Network
Detailed chemical simulator
DNA Parts Sequence
Assembly Instructions
Testing
Cells
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
Motif-Based Compilation

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)))
arg0
GFP
value
16
Motif-Based Compilation

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)))
IPTG
LacI
value
17
Motif-Based Compilation

Functional program gives dataflow computation:
(green (not (IPTG)))
18
Motif-Based Compilation

Functional program gives dataflow computation:
(green (not (IPTG)))
IPTG
not
green
19
Motif-Based Compilation

Operators translated to motifs:
IPTG
not
green
20
Motif-Based Compilation

Operators translated to motifs:
IPTG
not
green
IPTG
A
LacI
outputs
arg0
B
outputs arg0
GFP
outputs
21
Motif-Based Compilation

Operators translated to motifs:
IPTG
not
green
IPTG
A
outputs
LacI
arg0
B
outputs arg0
GFP
outputs
IPTG
LacI
A
B
GFP
22
Optimization
IPTG
LacI
A
B
GFP
23
Optimization
IPTG
LacI
A
GFP
Copy Propagation
IPTG
LacI
B
A
B
GFP
24
Optimization
IPTG
LacI
A
A
B
GFP
Dead Code Elimination
IPTG
LacI
GFP
Copy Propagation
IPTG
LacI
B
A
GFP
25
Optimization
IPTG
LacI
A
A
A
GFP
GFP
Dead Code Elimination
IPTG
LacI
B
Dead Code Elimination
IPTG
LacI
GFP
Copy Propagation
IPTG
LacI
B
A
GFP
26
Complex System: Feedback Latch
(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)))
27
Complex System: Feedback Latch
(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)))
IPTG
GFP
LacI
B
aTc
TetR
I
D
I
C
J
A
F
E1
H
G
E2
J
Unoptimized: 15 functional units, 13 transcription factors
28
Optimization of Complex Designs
(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)))
IPTG
GFP
LacI
B
aTc
TetR
I
D
I
C
J
A
F
E1
H
G
E2
J
Unoptimized: 15 functional units, 13 transcription factors
Copy Propagation29
Optimization of Complex Designs
(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)))
IPTG
GFP
B
E1
I
F
LacI TetR
aTc
D
I
C
J
H
A
G
J
Unoptimized: 15 functional units, 13 transcription factors
Common Subexp. Elim.
30
Optimization of Complex Designs
(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)))
IPTG
GFP
B
E1
I
F
LacI TetR
aTc
D
I
C
H
J
G
A
J
H
Unoptimized: 15 functional units, 13 transcription factors
NOR Compression31
Optimization of Complex Designs
(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)))
IPTG
GFP
E1
I
F
LacI TetR
aTc
I
H
G
H
Unoptimized: 15 functional units, 13 transcription factors
Dead Code Elimination
32
Optimization of Complex Designs
(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)))
IPTG
GFP
E1
I
F
LacI TetR
aTc
I
H
G
H
Unoptimized: 15 functional units, 13 transcription factors
Copy Propagation33
Optimization of Complex Designs
(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)))
IPTG
GFP
E1
G
I
H
I
F
LacI TetR
aTc
H
Unoptimized: 15 functional units, 13 transcription factors
Common Subexp. Elim.
34
Optimization of Complex Designs
(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)))
IPTG
GFP
H
I
F
LacI TetR
aTc
I
H
Unoptimized: 15 functional units, 13 transcription factors
Dead Code Elimination
35
Optimization of Complex Designs
(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)))
IPTG
LacI TetR
I
F
H
I
GFP
H
aTc
Unoptimized: 15 functional units, 13 transcription factors
36
Optimization of Complex Designs
(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)))
IPTG
F
LacI TetR
I
GFP
H
aTc
H
F
I
Unoptimized: 15 functional units, 13 transcription factors
NOR Compression37
Optimization of Complex Designs
(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)))
IPTG
F
LacI TetR
GFP
H
aTc
H
F
Unoptimized: 15 functional units, 13 transcription factors
Dead Code Elimination
38
Optimization of Complex Designs
(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)))
IPTG
LacI TetR
F
GFP
aTc
H
F
H
Final Optimized:
5 functional units
4 transcription factors
Unoptimized: 15 functional units, 13 transcription factors
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
Realization with Characterized DNA parts
Dox
pHef1a
mKate
pHef1a
rtTA
Tre
EBFP
Tre
pLac
Hef1a-LacO1Oid
EYFP
41
Onward Through the Tool-Chain…
(yellow (not (cyan (Dox))))
Organism Level
Description
Dox
cyan
not
High level
simulator
yellow
High Level
Description
Dox
If detect explosives:
emit signal
If signal > threshold:
glow red
Coarse chemical
simulator
rtTA
CFP
B
Abstract Genetic
Regulatory Network
EYFP
Detailed chemical
simulator
DNA Parts
Sequence
pHef1a
rtTA
pTre
CFP
pTre
LacI
mirff4 pHef1a- EYFP
LacO1Oid
4xff4
Assembly
Instructions
Testing
Cells
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