1. Kaifeng Chen 04.22.2013 Institute for Theoretical Physics Synthetic Biology with Engineering Tools 1 Francis Chen

2. All models are wrong, but some are useful. 2 Francis Chen

3. Outline Introduction Synthetic Biology: Why “Synthetic”? Conceptions in Engineering iGEM Competition What Can We Do Wet Lab Experiments Dry Lab Software 3 Francis Chen

4. 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 4 Francis Chen

5. 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 INTRODUCTION 5 Francis Chen

6. Introduction 6 Francis Chen

7. Conceptions in Engineering 7 Francis Chen

8. Conceptions in Engineering 8 Francis Chen

9. Conceptions in Engineering Standardization (Input, output) Modularity Encapsulation 9 Francis Chen

10. iGEM Competition international Genetically Engineered Machine Regional Jamboree & World Jamboree 10 Francis Chen

11. iGEM Competition Engineering Biology Synthetic Biology 11 Francis Chen

12. iGEM Competition Engineering Biology Synthetic Biology WHAT CAN WE DO 12 Francis Chen

13. What Can We Do Wet Lab Teams BioBricks New Applications Challenges Biobricks Functional partsplasmid 13 Francis Chen

14. What Can We Do Dry Lab Teams Powerful Function User Friendly Clean GUI Seamless Design Searching Browser Computation & Simulation CAD Software 14 Francis Chen

15. What Can We Do Software Developers 15 Francis Chen

16. What Can We Do 16 Francis Chen

17. What Can We Do 17 Francis Chen

18. What Can We Do 18 Francis Chen

19. What Can We Do HOW CAN WE DO 19 Francis Chen

20. Logic Gates Feed forward Loop Sensor …… 20 Francis Chen

21. Artificial Intelligence Genetic Algorithm (GA) Particle Swarm Optimization (PSO) Ant Colony Optimization (ACO) Simulated Annealing (SA) 21 Francis Chen

22. Toggle Switch & Oscillator 22 Francis Chen

23. Machine Learning Decision Tree Neural Network Patter Recognition Bayes Network Data Mining ………. 23 Francis Chen

24. Language & Format Coding Language: C, C++, Java, Python, Perl Storing Formats SBML, SBOL, Eugene Wiki Development HTML, CSS, JavaScript 24 Francis Chen

25. Language & Format Coding Language: C, C++, Java, Python, Perl Storing Formats SBML, SBOL, Eugene Wiki Development HTML, CSS, JavaScript FORWARD & REVERSE ENGINEERING 25 Francis Chen

26. Genetic Regulatory Network Node: Species Lines: Reactions or Regulations 26 Francis Chen

27. Forward Engineering System Experiments Results 27 Francis Chen

28. Forward Engineering System Experiments Results 28 Francis Chen

29. Reverse Engineering System Results Mathematic Model 29 Francis Chen

30. Summary Ideas about Synthetic Biology Methods in Synthetic Biology Combination with Engineering & Computer Science GRN Modeling Forward & Reverse Engineering www.stanford.edu/~kfchen Download Files : 30 Francis Chen

31. 31 Francis Chen