Synthetic Biology with
Engineering Tools
Kaifeng Chen
04.22.2013
Institute for Theoretical Physics
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All models are wrong,
but some are useful.
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Outline
 Introduction
Synthetic Biology: Why “Synthetic”?
Conceptions in Engineering
iGEM Competition
 What Can We Do
Wet Lab Experiments
Dry Lab Software
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Outline
 How Can We Do
Methods in Engineering
(Logic Gates, Information Process)
Methods in Computer Science
(Machine Learning, Pattern Recognition, Data Mining)
 Forward & Reverse Engineering
Genetic Regulatory Network
Forward Engineering
Reverse Engineering
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Outline
 How Can We Do
Methods in Engineering
(Logic Gates, Information Process)
INTRODUCTION
Methods in Computer Science
(Machine Learning, Pattern Recognition, Data Mining)
 Forward & Reverse Engineering
Genetic Regulatory Network
Forward Engineering
Reverse Engineering
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Introduction
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Conceptions in Engineering
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Conceptions in Engineering
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Conceptions in Engineering
 Standardization
(Input, output)
 Modularity
 Encapsulation
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iGEM Competition
 international Genetically Engineered Machine
 Regional Jamboree & World Jamboree
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iGEM Competition
Engineering
Synthetic Biology
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Biology
iGEM Competition
WHAT CAN WE DO
Engineering
Synthetic Biology
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Biology
What Can We Do
 Wet Lab Teams



BioBricks
New Applications
Challenges
Biobricks
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Functional parts
plasmid
What Can We Do
 Dry Lab Teams




Powerful Function
User Friendly
Clean GUI
Seamless Design
Software
Searching Browser
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Computation & Simulation
CAD
What Can We Do
Software Developers
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What Can We Do
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What Can We Do
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What Can We Do
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What Can We Do
HOW CAN WE DO
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Logic Gates
Feed forward Loop
Sensor ……
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Artificial Intelligence
 Genetic Algorithm (GA)
 Particle Swarm Optimization (PSO)
 Ant Colony Optimization (ACO)
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 Simulated Annealing (SA)
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Toggle Switch & Oscillator
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Machine Learning
 Decision Tree
 Neural Network
 Patter Recognition
 Bayes Network
 Data Mining
 ……….
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Language & Format
 Coding Language:
C, C++, Java, Python, Perl
 Storing Formats
SBML, SBOL, Eugene
 Wiki Development
HTML, CSS, JavaScript
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Language & Format
 Coding Language:
C, C++, Java, Python, Perl
FORWARD & REVERSE
SBML, SBOL, Eugene
ENGINEERING
 Storing Formats
 Wiki Development
HTML, CSS, JavaScript
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Genetic Regulatory Network
Node: Species
Lines: Reactions or
Regulations
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Forward Engineering
System
Results
Experiments
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Forward Engineering
𝑑𝑋
= 𝑓 𝑋, 𝜃
𝑑𝑡
System
Results
Experiments
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Reverse Engineering
Mathematic
Model
System
Results
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Summary
 Ideas about Synthetic Biology
 Methods in Synthetic Biology
 Combination with Engineering & Computer Science
 GRN Modeling
 Forward & Reverse Engineering
Download Files :
www.stanford.edu/~kfchen
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