CHE.496/2008/Assignments

Assignment 1

1. Chapter 1: Philosophical viewpoints on the new biology
2. Chapter 2: Basics of molecular biology, genetic engineering and metabolic engineering

Assignment 2

1. Intelligent design
2. Extreme genetic engineering: An introduction to synthetic biology
3. A partnership between biology and engineering

Assignment 3

1. Idempotent vector design for standard assembly of biobricks
2. Foundations for engineering biology
3. Synthetic biology–putting engineering into biology

Assignment 4

1. Genetic parts to program bacteria
2. Designing biological systems
3. Biology by design: Reduction and synthesis of cellular components and behavior

Assignment 5

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

Assignment 6

1. Synthetic biology: New engineering rules for an emerging discipline
2. Programming and engineering biological networks
3. Fast, cheap and somewhat in control

Assignment 7

1. Systems biology as a foundation for genome-scale synthetic biology
2. Chapter 3: High-throughput technologies and functional genomics
3. Chapter 4: High-throughout proteomics

Assignment 8

1. Chapter 5: Bioinformatics and phylogenetics
2. Chapter 7: From recombinant genes to recombinant genomes for systems biology
3. Chapter 8: In silico genome-scale metabolic models: the constraint-based approach

Assignment 9

1. Chapter 9: Modeling the dynamics of genetic regulatory networks
2. Chapter 12: Systems biotechnology: applications of in silico modeling
3. Chapter 13: Synthetic biology: putting engineering into bioengineering

Assignment 10

1. Chapter 14: Rationales of gene design and de novo gene construction
2. Chapter 16: Synthetic genetic networks
3. Chapter 21: Systems biology and synthetic biology in the post genomic era

Assignment 11

1. DNA synthesis and biological security
2. The promises and perils of synthetic biology
3. Synthetic biology: Navigating the challenges ahead

Assignment 12

1. Economics of synthetic biology
2. Synthetic biology: Caught between property rights, the public domain, & the commons