Difference between revisions of "Intertech:iSB2008:Materials"

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''' Basic Synthetic Biology Circuits'''
''' Basic Synthetic Biology Circuits'''
(based on the [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Computer Modelling Practicals] lecture by V. Rouilly at Imperial college)
(based on the [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Computer Modelling Practicals] lecture by Vincent Rouilly at Imperial College)

Revision as of 07:41, 28 May 2008

introduction to Synthetic Biology 2008


Home        Syllabus & Materials        Resources        Help & Attribution       


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


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


  • 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, 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


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

Basic Synthetic Biology Circuits

(based on the Computer Modelling Practicals lecture by Vincent Rouilly at Imperial College)

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