CHE.496/2008/Assignments

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==Assigned Readings==
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==Assignment 1: Synthetic biology overview==
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====Assignment 1: Synthetic biology overview====
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# Extreme genetic engineering: An introduction to synthetic biology
# Extreme genetic engineering: An introduction to synthetic biology
# Intelligent Life
# Intelligent Life
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==Assignment 2: Foundational technologies==
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====Assignment 2: Foundational technologies====
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# Foundations for engineering biology
# Foundations for engineering biology
# A partnership between biology and engineering
# A partnership between biology and engineering
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==Assignment 3: Engineering principles==
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====Assignment 3: Engineering principles====
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# Synthetic biology - putting engineering into biology
# Synthetic biology - putting engineering into biology
# Synthetic biology: New engineering rules for an emerging discipline
# Synthetic biology: New engineering rules for an emerging discipline
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==Assignment 4: Biobricks and genetic programming==
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====Assignment 4: Biobricks and genetic programming====
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# Idempotent vector design for standard assembly of biobricks
# Idempotent vector design for standard assembly of biobricks
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# Biology by design: Reduction and synthesis of cellular components and behavior
# Biology by design: Reduction and synthesis of cellular components and behavior
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==Assignment 5: Bioinformatics and systems biology==
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====Assignment 5: Bioinformatics and systems biology====
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# Systems biology as a foundation for genome-scale synthetic biology
# Systems biology as a foundation for genome-scale synthetic biology
# Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
# Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
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==Assignment 6: Practical applications==
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====Assignment 6: Practical applications====
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# Advances in synthetic biology: on the path from prototypes to applications
# Advances in synthetic biology: on the path from prototypes to applications
# Molecular switches for cellular sensors
# Molecular switches for cellular sensors
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==Assignment 7: Societal implications==
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====Assignment 7: Societal implications====
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# The promises and perils of synthetic biology
# The promises and perils of synthetic biology
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# Characterization of the reconstructed 1918 Spanish influenza pandemic virus
# Characterization of the reconstructed 1918 Spanish influenza pandemic virus
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==Assignment 8: Synthetic genes, biological machines, and minimal genomes==
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====Assignment 8: Synthetic genes, biological machines, and minimal genomes====
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# Genetic parts to program bacteria
# Genetic parts to program bacteria
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# Global transposon mutagenesis and a minimal mycoplasma genome
# Global transposon mutagenesis and a minimal mycoplasma genome
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==Assignment 9: Cases studies in synthetic biology==
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====Assignment 9: Cases studies in synthetic biology====
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# Environmentally controlled invasion of cancer cells by engineered bacteria
# Environmentally controlled invasion of cancer cells by engineered bacteria
# Production of isoprenoid pharmaceuticals by engineered microbes
# Production of isoprenoid pharmaceuticals by engineered microbes
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</font>
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==Assignment 10: Genetic circuit engineering==
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====Assignment 10: Genetic circuit engineering====
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# A synthetic oscillatory network of transcriptional regulators
# A synthetic oscillatory network of transcriptional regulators
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# Engineered gene circuits
# Engineered gene circuits
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==Assignment 11: Metabolic pathway engineering==
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====Assignment 11: Metabolic pathway engineering====
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# Bioengineering novel in vitro metabolic pathways using synthetic biology
# Bioengineering novel in vitro metabolic pathways using synthetic biology
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==Assignment 12: Biological network engineering==
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====Assignment 12: Biological network engineering====
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# Programming and engineering biological networks
# Programming and engineering biological networks
# Modular approaches to expanding the functions of living matter
# Modular approaches to expanding the functions of living matter
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==Assignment 13: Systems biology and the omic sciences==
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====Assignment 13: Systems biology and the omic sciences====
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==Assignment 14: Mathematical biology==
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====Assignment 14: Mathematical biology====
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==Assignment 15: Computational biology==
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====Assignment 15: Computational biology====
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==Assignment 16: Metabolic flux analysis==
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====Assignment 16: Metabolic flux analysis====
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==Assignment 17: Genome-scale metabolic models==
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====Assignment 17: Genome-scale metabolic models====
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==Assignment 18: Modeling genetic regulatory networks==
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====Assignment 18: Modeling genetic regulatory networks====
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==Assignment 19: Systems biotechnology==
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====Assignment 19: Systems biotechnology====
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Revision as of 13:36, 8 November 2007

CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

  1. Extreme genetic engineering: An introduction to synthetic biology
  2. Intelligent Life

Assignment 2: Foundational technologies

  1. Foundations for engineering biology
  2. A partnership between biology and engineering

Assignment 3: Engineering principles

  1. Synthetic biology - putting engineering into biology
  2. Synthetic biology: New engineering rules for an emerging discipline

Assignment 4: Biobricks and genetic programming

  1. Idempotent vector design for standard assembly of biobricks
  2. Designing biological systems
  3. Biology by design: Reduction and synthesis of cellular components and behavior

Assignment 5: Bioinformatics and systems biology

  1. Systems biology as a foundation for genome-scale synthetic biology
  2. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information

Assignment 6: Practical applications

  1. Advances in synthetic biology: on the path from prototypes to applications
  2. Molecular switches for cellular sensors

Assignment 7: Societal implications

  1. The promises and perils of synthetic biology
  2. Synthetic biology: Navigating the challenges ahead
  3. Synthetic biology: Caught between property rights, the public domain, & the commons
  4. Economics of synthetic biology
  5. DNA synthesis and biological security
  6. Characterization of the reconstructed 1918 Spanish influenza pandemic virus

Assignment 8: Synthetic genes, biological machines, and minimal genomes

  1. Genetic parts to program bacteria
  2. Codon bias and heterologous protein expression
  3. Fast, cheap and somewhat in control
  4. Global transposon mutagenesis and a minimal mycoplasma genome

Assignment 9: Cases studies in synthetic biology

  1. Environmentally controlled invasion of cancer cells by engineered bacteria
  2. Production of isoprenoid pharmaceuticals by engineered microbes

Assignment 10: Genetic circuit engineering

  1. A synthetic oscillatory network of transcriptional regulators
  2. Construction of a genetic toggle switch in Escherichia coli
  3. Engineered gene circuits

Assignment 11: Metabolic pathway engineering

  1. Bioengineering novel in vitro metabolic pathways using synthetic biology

Assignment 12: Biological network engineering

  1. Programming and engineering biological networks
  2. Modular approaches to expanding the functions of living matter

Assignment 13: Systems biology and the omic sciences

Assignment 14: Mathematical biology

Assignment 15: Computational biology

Assignment 16: Metabolic flux analysis

Assignment 17: Genome-scale metabolic models

Assignment 18: Modeling genetic regulatory networks

Assignment 19: Systems biotechnology

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