Synthetic Biology with Engineering Tools

Kaifeng Chen04.22.2013Institute for Theoretical PhysicsSynthetic Biology withEngineering Tools1Francis Chen1Francis ChenAll models are wrong,but some are useful.2Francis ChenOutlineIntroduction Synthetic Biology: Why Synthetic? Conceptions in Engineering iGEM Competition

What Can We Do Wet Lab Experiments Dry Lab Software3Francis ChenOutlineHow 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 Engineering4Francis ChenOutlineHow 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 EngineeringINTRODUCTION5Francis ChenIntroduction

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Conceptions in Engineering

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Conceptions in Engineering

8Francis ChenConceptions in EngineeringStandardization (Input, output)ModularityEncapsulation9Francis CheniGEM Competitioninternational Genetically Engineered MachineRegional Jamboree & World Jamboree

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iGEM Competition

EngineeringBiologySynthetic Biology11Francis Chen

iGEM Competition

EngineeringBiologySynthetic BiologyWHAT CAN WE DO12Francis ChenWhat Can We DoWet Lab Teams BioBricks New Applications ChallengesBiobricksFunctional partsplasmid13Francis ChenWhat Can We DoDry Lab Teams Powerful Function User Friendly Clean GUI Seamless DesignSearching BrowserComputation & SimulationCADSoftware14Francis ChenWhat Can We Do

Software Developers15Francis ChenWhat Can We Do

16Francis ChenWhat Can We Do

17Francis ChenWhat Can We Do

18Francis ChenWhat Can We Do

HOW CAN WE DO19Francis ChenLogic Gates

Feed forward LoopSensor 20Francis ChenArtificial IntelligenceGenetic Algorithm (GA)Particle Swarm Optimization (PSO)Ant Colony Optimization (ACO)Simulated Annealing (SA)

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Toggle Switch & Oscillator

22Francis ChenMachine LearningDecision TreeNeural NetworkPatter RecognitionBayes NetworkData Mining.23Francis ChenLanguage & FormatCoding Language: C, C++, Java, Python, Perl

Storing Formats SBML, SBOL, Eugene

Wiki Development HTML, CSS, JavaScript

24Francis ChenLanguage & FormatCoding Language: C, C++, Java, Python, Perl

Storing Formats SBML, SBOL, Eugene

Wiki Development HTML, CSS, JavaScript

FORWARD & REVERSE ENGINEERING25Francis ChenGenetic Regulatory Network

Node: Species

Lines: Reactions or Regulations26Francis ChenForward Engineering

SystemExperimentsResults27Francis ChenForward Engineering

SystemExperimentsResults

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Reverse Engineering

SystemResultsMathematic Model

29Francis ChenSummaryIdeas about Synthetic BiologyMethods in Synthetic BiologyCombination with Engineering & Computer ScienceGRN ModelingForward & Reverse Engineeringwww.stanford.edu/~kfchenDownload Files :30Francis ChenThanks for listening31Francis Chen