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Kaifeng Chen 04.22.2013 Institute for Theoretical Physics Synthetic Biology with Engineering Tools 1 Francis Chen
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All models are wrong, but some are useful. 2 Francis Chen
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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 3 Francis Chen
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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 4 Francis Chen
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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 INTRODUCTION 5 Francis Chen
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Introduction 6 Francis Chen
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Conceptions in Engineering 7 Francis Chen
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Conceptions in Engineering 8 Francis Chen
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Conceptions in Engineering Standardization (Input, output) Modularity Encapsulation 9 Francis Chen
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iGEM Competition international Genetically Engineered Machine Regional Jamboree & World Jamboree 10 Francis Chen
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iGEM Competition Engineering Biology Synthetic Biology 11 Francis Chen
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iGEM Competition Engineering Biology Synthetic Biology WHAT CAN WE DO 12 Francis Chen
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What Can We Do Wet Lab Teams BioBricks New Applications Challenges Biobricks Functional partsplasmid 13 Francis Chen
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What Can We Do Dry Lab Teams Powerful Function User Friendly Clean GUI Seamless Design Searching Browser Computation & Simulation CAD Software 14 Francis Chen
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What Can We Do Software Developers 15 Francis Chen
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What Can We Do 16 Francis Chen
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What Can We Do 17 Francis Chen
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What Can We Do 18 Francis Chen
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What Can We Do HOW CAN WE DO 19 Francis Chen
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Logic Gates Feed forward Loop Sensor …… 20 Francis Chen
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Artificial Intelligence Genetic Algorithm (GA) Particle Swarm Optimization (PSO) Ant Colony Optimization (ACO) Simulated Annealing (SA) 21 Francis Chen
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Toggle Switch & Oscillator 22 Francis Chen
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Machine Learning Decision Tree Neural Network Patter Recognition Bayes Network Data Mining ………. 23 Francis Chen
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Language & Format Coding Language: C, C++, Java, Python, Perl Storing Formats SBML, SBOL, Eugene Wiki Development HTML, CSS, JavaScript 24 Francis Chen
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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
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Genetic Regulatory Network Node: Species Lines: Reactions or Regulations 26 Francis Chen
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Forward Engineering System Experiments Results 27 Francis Chen
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Forward Engineering System Experiments Results 28 Francis Chen
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Reverse Engineering System Results Mathematic Model 29 Francis Chen
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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
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31 Francis Chen
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