CHE.496/2008/Assignments

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====Assignment 1: Synthetic biology overview====
====Assignment 1: Synthetic biology overview====
<font color=blue>
<font color=blue>
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# Extreme genetic engineering: An introduction to synthetic biology
+
# '''Extreme genetic engineering: An introduction to synthetic biology
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# Intelligent Life
+
# '''Intelligent Life
</font>
</font>
====Assignment 2: Foundational technologies====
====Assignment 2: Foundational technologies====
<font color=blue>
<font color=blue>
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# Foundations for engineering biology
+
# '''Foundations for engineering biology
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# A partnership between biology and engineering
+
# '''A partnership between biology and engineering
</font>
</font>
====Assignment 3: Engineering principles====
====Assignment 3: Engineering principles====
<font color=blue>
<font color=blue>
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# Synthetic biology - putting engineering into biology
+
# '''Synthetic biology - putting engineering into biology
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# Synthetic biology: New engineering rules for an emerging discipline
+
# '''Synthetic biology: New engineering rules for an emerging discipline
</font>
</font>
====Assignment 4: Biobricks and genetic programming====
====Assignment 4: Biobricks and genetic programming====
<font color=blue>
<font color=blue>
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# Idempotent vector design for standard assembly of biobricks
+
# '''Idempotent vector design for standard assembly of biobricks
-
# Designing biological systems
+
# '''Designing biological systems
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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
</font>
</font>
====Assignment 5: Bioinformatics and systems biology====
====Assignment 5: Bioinformatics and systems biology====
<font color=blue>
<font color=blue>
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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
</font>
</font>
====Assignment 6: Practical applications====
====Assignment 6: Practical applications====
<font color=blue>
<font color=blue>
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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
</font>
</font>
====Assignment 7: Social implications====
====Assignment 7: Social implications====
<font color=blue>
<font color=blue>
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# The promises and perils of synthetic biology
+
# '''The promises and perils of synthetic biology
-
# Synthetic biology: Navigating the challenges ahead
+
# '''Synthetic biology: Navigating the challenges ahead
-
# Synthetic biology: Caught between property rights, the public domain, & the commons
+
# '''Synthetic biology: Caught between property rights, the public domain, & the commons
-
# Economics of synthetic biology
+
# '''Economics of synthetic biology
-
# DNA synthesis and biological security
+
# '''DNA synthesis and biological security
-
# Characterization of the reconstructed 1918 Spanish influenza pandemic virus
+
# '''Characterization of the reconstructed 1918 Spanish influenza pandemic virus
</font>
</font>
====Assignment 8: Synthetic genes, biological machines, and minimal genomes====
====Assignment 8: Synthetic genes, biological machines, and minimal genomes====
<font color=green>
<font color=green>
-
# Genetic parts to program bacteria
+
# '''Genetic parts to program bacteria
-
# Codon bias and heterologous protein expression
+
# '''Codon bias and heterologous protein expression
-
# Fast, cheap and somewhat in control
+
# '''Fast, cheap and somewhat in control
</font>
</font>
====Assignment 9: Dr. Craig Venter's minimal genome work====
====Assignment 9: Dr. Craig Venter's minimal genome work====
<font color=green>
<font color=green>
-
# Global transposon mutagenesis and a minimal mycoplasma genome
+
# '''Global transposon mutagenesis and a minimal mycoplasma genome
</font>
</font>
====Assignment 10: Dr. George Church's minimal cell work====
====Assignment 10: Dr. George Church's minimal cell work====
<font color=green>
<font color=green>
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# Toward synthesis of a minimal cell
+
# '''Toward synthesis of a minimal cell
</font>
</font>
====Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work====
====Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work====
<font color=green>
<font color=green>
-
# A synthetic oscillatory network of transcriptional regulators
+
# '''A synthetic oscillatory network of transcriptional regulators
</font>
</font>
====Assignment 12: Dr. Jim Collins' genetic circuit engineering work====
====Assignment 12: Dr. Jim Collins' genetic circuit engineering work====
<font color=green>
<font color=green>
-
# Construction of a genetic toggle switch in ''Escherichia coli''
+
# '''Construction of a genetic toggle switch in ''Escherichia coli''
-
# Engineered gene circuits
+
# '''Engineered gene circuits
</font>
</font>
====Assignment 13: Dr. Chris Voigt's genetic circuit engineering work====
====Assignment 13: Dr. Chris Voigt's genetic circuit engineering work====
<font color=green>
<font color=green>
-
# Environmentally controlled invasion of cancer cells by engineered bacteria
+
# '''Environmentally controlled invasion of cancer cells by engineered bacteria
-
# Environmental signal integration by a modular AND gate
+
# '''Environmental signal integration by a modular AND gate
</font>
</font>
====Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work====
====Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work====
<font color=green>
<font color=green>
-
# Production of isoprenoid pharmaceuticals by engineered microbes
+
# '''Production of isoprenoid pharmaceuticals by engineered microbes
</font>
</font>
====Assignment 15: Systems biology and the omic sciences====
====Assignment 15: Systems biology and the omic sciences====

Revision as of 16:57, 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: Social 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

Assignment 9: Dr. Craig Venter's minimal genome work

  1. Global transposon mutagenesis and a minimal mycoplasma genome

Assignment 10: Dr. George Church's minimal cell work

  1. Toward synthesis of a minimal cell

Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work

  1. A synthetic oscillatory network of transcriptional regulators

Assignment 12: Dr. Jim Collins' genetic circuit engineering work

  1. Construction of a genetic toggle switch in Escherichia coli
  2. Engineered gene circuits

Assignment 13: Dr. Chris Voigt's genetic circuit engineering work

  1. Environmentally controlled invasion of cancer cells by engineered bacteria
  2. Environmental signal integration by a modular AND gate

Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work

  1. Production of isoprenoid pharmaceuticals by engineered microbes

Assignment 15: Systems biology and the omic sciences

Assignment 16: Mathematical biology

Assignment 17: Computational biology

Assignment 18: Metabolic flux analysis

Assignment 19: Genome-scale metabolic models

Assignment 20: Modeling genetic regulatory networks

Assignment 21: Systems biotechnology

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