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Synthetic Biology for Programmers

Synthetic Biology for Programmers. Joshua D. Bruning. Examples. Photographic film Water that changes pH when exposed to arsenic Salmonella that secretes spider silk proteins instead of toxins Toggle switch. Science + Engineering. Convergence of biology and engineering. Representation.

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Synthetic Biology for Programmers

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  1. Synthetic Biology for Programmers Joshua D. Bruning

  2. Examples • Photographic film • Water that changes pH when exposed to arsenic • Salmonella that secretes spider silk proteins instead of toxins • Toggle switch

  3. Science + Engineering • Convergence of biology and engineering

  4. Representation • Base = bit

  5. Wetware • Software that Builds Hardware

  6. Reading (Sequencing) • Partial analysis (~1 million bp) • 2008: ~$1,000 • 2009: ~$300-$500 • Full human genome (~3 billion bp) • 2008: ~$350,000 • 2009: ~$99,000

  7. Writing (Synthesizing) • $1/bp • phiX-174: $5,386 • Smallpox: $186,102 • Human: ~$3,000,000,000

  8. Abstraction • Systems • Devices • Parts • DNA

  9. BioBricks • Open-source genetic parts • http://partsregistry.org • Long-term goal: to build a synthetic living organism that is completely understood

  10. Refactoring • Genetic programming vs. Structural programming • Bacteriophage T7

  11. Emulation • Graph theory • Boolean networks • Ordinary differential equations • Stochastic differential equations • Master equations

  12. Social Issues • Risk/Security • What’s wrong with the DNA God gave us? • Economics/Patents • Organization

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