BIOEN 424 in 2012

BIOEN 424  – Synthetic and Systems Biology Spring 2012
  

 Image from Synthetic biology: applications come of age Ahmad S. Khalil & James J. Collins Nature Reviews Genetics 11, 367-379 (May 2010) 

Syllabus

Every Monday, a two papers from the synthetic biology world will be dicussed.

WeekLecture Topics
1Introduction, Life as a Technology, Case study of a natural complex system: Lambda Phage
2Gene regulatory kinetics, review of Michaelian and Allosteric Kinetics, Generalized Kinetic Laws
3Review: Stoichiometry Matrices, System Equation, Modeling, Software, SBML
4Review Control Theory, H(0), Elasticities, Control Coefficients, Stability
5Motifs: Feedback, Feedforward Systems. Oscillators, Switches, adapters, and other beasts.
6Control of Metabolic Systems: Basic Principles of Flow Control; Front Loading of Control; Optimal Allocation of Protein in Flow Control; Tracking, Control and other Strategies in Metabolic Engineering

Start thinking about the term design project.
7Control of Metabolic Systems
8Invited Speaker: Impedance, Fan-Out and Modularity in Synthetic Biology
9Flux and Moiety Constraints; Elementary Modes and Flux Balance Analysis
10Team Project Presentations

Grading:

Oral Presentations:    15% (Credit/No Credit)
Assignments:            25%
Midterm:                   25%
Design Project:         35%

Possible Textbooks:

No official text book but the following can be recommended:

   * An Introduction to Systems Biology: Design Principles of Biological Circuits (ISBN-10: 1584886420), U Alon
   * Systems Biology: A Textbook. (ISBN-10: 3527318747) Klipp et al
   * Engineering Genetic Circuits (ISBN-10: 1420083244) Myers.
   * Enzyme Kinetics for Systems Biology. Sauro HM ($39 but Available for approximately $6 to students in this course)
   * Control Theory for Biologists 

   * Notes will be provided on this Wiki

Class Notes

Latex Mini-Tutorial

Simulation Environment for 424: Jarnac 3.16 (Windows installer, requires SBW to operate new EasySIm interface)

Jarnac comes with built in help but here is a separate document that might be helpful:

Jarnac Notes (v0.82)

List of Jarnac Methods

Network Motifs

Assignments

Assignment 1:

Fill in the regulatory loops in the Lambda Phage plasmid figure (Only consider 11 to 6 on the plasmid).

Assignment 2 (update April 10, 7.48 pm to fix one typos in q6) – deadline 11th April.

Assignment 3

Assignment 4 (Due Friday 27th of April)

Assignment 5: (Due Friday 11th of May) Refer to Control Theory for Biologists

Answer the following questions in chapter 10: 1, 2, 4, 6, 7, 8, 9, 13, 14, 17

Answer the following questions in chapter 11: 3, 5, 7, 8, 11

There will be no midterm, instead I will release this week (Week 7) a take-home exam. The due date for this is the end of Week 9.

Download take Home Exam

Making a Killer Flu

End of Term Project

The course incorporates a team based design component. Teams are expected to provide the designs for a novel cellular molecular device. Teams will work in pairs and present their work in class and in the form of a final report. The report will be expected to include the following sections (See design project template for details): Title, Author names and date; Abstract; Introduction; Overview; Product Design Spec; Internal Design Spec; Validation and Test Implementation (in silico); in vivo Implementation Details including estimated construction costs, time lines and suggested assembly methods; Conclusion; References.

Format document for design project Download

Presentation will be made on the 30th of May (Wednesday)

Oral Presentations:

Week 2: Pick one paper from this selection

1.  Distributed biological computation with multicellular engineered networks. 
2.  A synthetic low-frequency mammalian oscillator
3.  Beyond directed evolution: Darwinian selection as a tool for synthetic biology
4.  Genetdes: automatic design of transcriptional networks
5.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
6.  Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition
7.  Functional roles for noise in genetic circuits

Week 3: Pick one paper from this selection

1.  Distributed biological computation with multicellular engineered networks. 
2.  A synthetic low-frequency mammalian oscillator
3.  Genetdes: automatic design of transcriptional networks
4.  Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition
5.  Functional roles for noise in genetic circuits 
6.  Multichromatic Control of Gene Expression in Escherichia coli
7.  Minimal genetic device with multiple tunable functions
8.  Isoprenoid Pathway Optimization for Taxol Precursor Overproduction inEscherichia coli

Week 4: Pick one paper from this selection

1.  A synthetic low-frequency mammalian oscillator
2.  Genetdes: automatic design of transcriptional networks
3.  Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition
4.  Multichromatic Control of Gene Expression in Escherichia coli
5.  Minimal genetic device with multiple tunable functions
6.  Isoprenoid Pathway Optimization for Taxol Precursor Overproduction inEscherichia coli

 Week 5: Pick one paper from this selection

1. Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
2. Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat 
3. A genetically encoded fluorescent reporter of ATP:ADP ratio
4. Toward scalable parts families for predictable design of biological circuits
5. Microfluidic devices for measuring gene network dynamics in single cells
6. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass2.  
7. Genetdes: automatic design of transcriptional networks
8. Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition
9. Minimal genetic device with multiple tunable functions
10. Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

Week 6: Pick one paper from this selection

1. Rationally designed families of orthogonal RNA regulators of translation
2. Programming cells by multiplex genome engineering and accelerated evolution
3. Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
3. Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat 
4. A genetically encoded fluorescent reporter of ATP:ADP ratio
5. Toward scalable parts families for predictable design of biological circuits
6. Microfluidic devices for measuring gene network dynamics in single cells
7. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass2.  
8. Genetdes: automatic design of transcriptional networks
9. Isoprenoid Pathway Optimization for Taxol Precursor Overproduction inEscherichia coli 

Final Week

1. Rewritable digital data storage in live cells via engineered control of recombination directionality
2. Programming cells by multiplex genome engineering and accelerated evolution
3. Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
4. Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat 
5. Toward scalable parts families for predictable design of biological circuits
6. Microfluidic devices for measuring gene network dynamics in single cells
7. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
8. Emergent cooperation in microbial metabolism
9. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ 
10.  Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination
11.  Higher-Order Cellular Information Processing with Synthetic RNA Devices
13. Pulsed feedback defers cellular differentiation
14 Stochastic Pulse Regulation in Bacterial Stress Response

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