Intertech:iSB2008:Materials

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'''Control theory'''
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[[Media:IT-2A Control Theory.pdf|'''Control theory''']]
* Introduction
* Introduction
* Types od controllers
* Types od controllers
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'''Electronics'''
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[[Media:IT-3A Electronics.pdf|'''Electronics''']]
* Introduction
* Introduction
* Boolean algebras
* Boolean algebras
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'''Error Theory'''
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[[Media:IT-4A Error theory.pdf|'''Error Theory''']]
* Introduction to measurement theory
* Introduction to measurement theory
* Error theroy description
* Error theroy description
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'''Programming in Matlab'''
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[[Media:5A Programing in Mathlab.pdf|'''Programming in Matlab''']]
* Introduction to programming languages
* Introduction to programming languages
* Basic MatLab operations
* Basic MatLab operations
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'''Flow of genetic information'''
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[[Media:IT-2B Flow of Genetic Information.pdf|'''Flow of genetic information''']]
* Elements
* Elements
* Nucelic acid – DNA and RNA
* Nucelic acid – DNA and RNA
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'''Genetic regulation'''
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[[Media:IT-3B genetic regulation.pdf|'''Genetic regulation''']]
* DNA regulation
* DNA regulation
* RNA regulation
* RNA regulation
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'''Communication with environment'''
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[[Media:IT-4B1 Communication with environment.pdf|'''Communication with environment''']]
* Signal transduction
* Signal transduction
* Signal  
* Signal  
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'''Kinetic Chemistry'''
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[[Media:IT-4B2 Kinetic Chemistry.pdf|'''Kinetic Chemistry''']]
* Definitions
* Definitions
* Law of mass action
* Law of mass action
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'''(Basic) Laboratory Techniques (of molecular biology)'''
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[[Media:IT-5B (Basic) Laboratory Techniques (in Molecular Biology).pdf|'''(Basic) Laboratory Techniques (of molecular biology)''']]
* DNA cloning
* DNA cloning
* Polymerase Chain Reaction
* Polymerase Chain Reaction

Revision as of 09:22, 28 May 2008

introduction to Synthetic Biology 2008

Home        Syllabus & Materials        Resources        Help & Attribution       

Syllabus

Syllabus of this course is divided in three parts. There is a group of topics that need to be known by biologists (or 'life science' people), then a bunch of topics that need to be known by engineers (or 'technical' people) and, finally, some lectures on 'what' is syntehtic biology and some examples of it.


Please note that all these slides are released under Creative Commons BY-SA

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Part 1 Training for biologists

Ordinary differential equations

  • Introduction
  • Basic concepts to understand an ODE
  • Description and properties of ODE
  • Solving ODE
  • Vector spaces
  • Dynamic systems


Control theory

  • Introduction
  • Types od controllers
  • Block diagram
  • Example of control
  • Laplace transform and transfer function
  • Frequency domain
  • Examples


Electronics

  • Introduction
  • Boolean algebras
  • Logical gates
  • Representation of boolean functions
  • Karnaugh maps


Error Theory

  • Introduction to measurement theory
  • Error theroy description
  • Types of errors
  • Evaluation of the error in an experimental measurement
  • Minimal square fit
  • Obtaining relations from experimental data


Programming in Matlab

  • Introduction to programming languages
  • Basic MatLab operations
  • Programming in Matlab
  • Solving ODE with Matlab

Part 2 Training for engineers

Cell

  • Cell, definition
  • Basic elements
  • Eukaryotes
  • Prokaryotes
  • Metabolism


Flow of genetic information

  • Elements
  • Nucelic acid – DNA and RNA
  • Amino acid – proteins
  • Central Dogma of Molecular Biology
  • Dogma, revisited
  • Horizontal transference


Genetic regulation

  • DNA regulation
  • RNA regulation
  • Protein regulation
  • Global regulatory mechanisms:


Communication with environment

  • Signal transduction
  • Signal
  • Receptor
  • Transducer
  • Actuator
  • Examples


Kinetic Chemistry

  • Definitions
  • Law of mass action
  • Enzyme-catalyzed reactions
  • Hill equation: allosterism
  • Hill equation in gene modelling


(Basic) Laboratory Techniques (of molecular biology)

  • DNA cloning
  • Polymerase Chain Reaction
  • Gel electrophoresis
  • Reading and writing DNA
  • Molecular hybridization
  • rewriting DNA: mutations
  • arrays


Part 3 Training in Synthetic Biology

Introduction to Synthetic Biology

  • Introduction
  • Synthetic Biology evolution
  • Some examples
  • Biology and Engineering: the paradigm of Synthetic biology
  • Systems Biology work
  • Synthetic gene regulatory systems


Standards

  • Building a composable DNA library
  • Registry
  • Parts
  • Signal carrier
  • Modularity
  • Looking for abstraction
  • Abstraction hierarchy


Basic Synthetic Biology Circuits


Synthetic Biology works

  • Toggle switch
  • Repressilator
  • Counting machine - ETH iGEM 2005
  • Memory device - ETH iGEM 2007
  • Cell free system - Imperial iGEM 2007
  • Synthetic pattern formation
  • Artifitial quorum sensing
  • Artemisinin production
Personal tools