CAD Tool

1
CAD Tool
Brians Automated Modular Biochemical
Instantiator (BAMBI)
Inputs

• Names of types.
• Functional dependencies.
• Probability distribution on outcomes.

Outputs

• Reactions implementing specification.
• Measures of accuracy and robustness.

2
Natural Stochasticity
Lambda Bacteriophage (Adam Arkin, 1998)
Hijack (Lysis)
Stealth (Lysogeny)
3
Natural Stochasticity
Portfolio of Responses
Prob. 0.2
Prob. 0.8
4
Modeling Natural Systems
Lambda Bacteriophage (Adam Arkin, 1998)

• Real model 117 reactions in 61 types.
• Our synthetic model 19 reactions in 17 types.

Curve-fits for data from Monte Carlo simulations
for both the natural and synthetic models,
sweeping the quantity of the input type moi from
1 through 10.
5
Synthesizing Stochasticity
Synthesizing Stochasticity in Biochemical Systems

• (potential) Applicationsbiochemical sensing,
  drug production, disease treatment.
• (immediate) Impetus framework for analyzing and
  characterizing the stochastic behavior of natural
  biological systems.

6
Reduced-Order Modeling
Lambda Bacteriophage (Adam Arkin, 1998)

• Real model 117 reactions in 61 types.
• Our synthetic model 19 reactions in 17 types.

Curve-fits for data from Monte Carlo simulations
for both the natural and synthetic models,
sweeping the quantity of the input type moi from
1 through 10.
7
Natural Stochasticity
Lambda Bacteriophage (Arkin et al., 1998)
Portfolio of Responses
Lysis
Lysogeny
Prob. 0.2
Prob. 0.8
8
Natural Stochasticity
Lambda Bacteriophage (Arkin et al., 1998)
lysis
lysogeny
9
Synthesizing Stochasticity
Lambda Bacteriophage (Arkin et al., 1998)
Synthesizing withBAMBI

• Real model 117 reactions in 61 types.
• Our synthetic model 19 reactions in 17 types.

10
Synthesis Results
Curve-fits for data from Monte Carlo simulations
for both the natural and synthetic models,
sweeping the quantity of the input type moi from
1 through 10.