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Synthetic Biology with Engineering Tools

Synthetic Biology with Engineering Tools. Kaifeng Chen 04.22.2013 Institute for Theoretical Physics. All models are wrong,. but some are useful. Outline. Introduction Synthetic Biology: Why “Synthetic”? Conceptions in Engineering iGEM Competition What Can We Do

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Synthetic Biology with Engineering Tools

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

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

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

  6. Introduction Francis Chen

  7. Conceptions in Engineering Francis Chen

  8. Conceptions in Engineering Francis Chen

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

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

  11. iGEM Competition Engineering Biology Synthetic Biology Francis Chen

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

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

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

  15. What Can We Do Software Developers Francis Chen

  16. What Can We Do Francis Chen

  17. What Can We Do Francis Chen

  18. What Can We Do Francis Chen

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

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

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

  22. Toggle Switch & Oscillator Francis Chen

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

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

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

  27. Forward Engineering System Results Experiments Francis Chen

  28. Forward Engineering System Results Experiments Francis Chen

  29. Reverse Engineering Mathematic Model System Results Francis Chen

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

  31. Thanks for listening Francis Chen

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