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| - | '''Introduction to Synthetic Biology''' | + | [[Media:IT-6 Introduction to Synthetic Biology.pdf|'''Introduction to Synthetic Biology''']] |
| | * Introduction | | * Introduction |
| | * Synthetic Biology evolution | | * Synthetic Biology evolution |
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| - | '''Standards''' | + | [[Media:IT-7 standards.pdf|'''Standards''']] |
| | * Building a composable DNA library | | * Building a composable DNA library |
| | * Registry | | * Registry |
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| | ''' Basic Synthetic Biology Circuits''' | | ''' Basic Synthetic Biology Circuits''' |
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| | + | (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) |
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| - | '''Synthetic Biology works''' | + | |
| | + | [[Media:IT-9 Synthetic Biology works.pdf|'''Synthetic Biology works''']] |
| | * Toggle switch | | * Toggle switch |
| | * Repressilator | | * Repressilator |
Revision as of 09:30, 28 May 2008
introduction to Synthetic Biology 2008
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.
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
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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
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Part 3 Training in Synthetic Biology
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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
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Basic Synthetic Biology Circuits
(based on the Computer Modelling Practicals lecture by V. 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
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