Intertech:Synthetic Biology course

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We have decided to prepare a course on 'Introduction on Synthetic Biology'.

(if you want to learn about more courses around the world go here)

The aim of this course is diverse.

  • First, is a way to organize the series of talks and lectures that we think should be taken by a given iGEM participant.
  • Second, is a way to gather educational material focused on people that want to have a broader perspective of Synthetic Biology.
  • Third, is a perfect starting point to whoever wants to take a step on this field.

The 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.

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 of bacteria)

  • 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
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