View source for Intertech:iSB2008:Materials

{{Template:ISB/2008}}

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==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.


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'''Please note that all these slides are released under [http://creativecommons.org/licenses/by-sa/3.0/ Creative Commons BY-SA]'''
http://i.creativecommons.org/l/by-sa/3.0/88x31.png</div>



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<font face="trebuchet ms" style="color:#047DB5" size="3">'''Part 1 Training for biologists'''</font><br>
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[[Media:IT-1A Ordinary differential equations.pdf|'''Ordinary differential equations''']]
* Introduction
* Basic concepts to understand an ODE 
* Description and properties of ODE
* Solving ODE
* Vector spaces
* Dynamic systems


[[Media:IT-2A Control Theory.pdf|'''Control theory''']]
* Introduction
* Types of controllers
* Block diagram
* Example of control
* Laplace transform and transfer function 
* Frequency domain
* Examples


[[Media:IT-3A Electronics.pdf|'''Electronics''']]
* Introduction
* Boolean algebras
* Logical gates
* Representation of boolean functions
* Karnaugh maps


[[Media:IT-4A Error theory.pdf|'''Error Theory''']]
* Introduction to measurement theory
* Error theory description
* Types of errors
* Evaluation of the error in an experimental measurement
* Minimal square fit
* Obtaining relations from experimental data 	


[[Media:5A Programing in Mathlab.pdf|'''Programming in Matlab''']]
* Introduction to programming languages
* Basic MatLab operations
* Programming in Matlab
* Solving ODE with Matlab

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<font face="trebuchet ms" style="color:#047DB5" size="3">'''Part 2 Training for engineers'''</font><br>
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[[Media:IT-1B cell.pdf|'''Cell''']]
* Cell, definition
* Basic elements
* Eukaryotes
* Prokaryotes
* Metabolism


[[Media:IT-2B Flow of Genetic Information.pdf|'''Flow of genetic information''']]
* Elements
* Nucleic acid – DNA and RNA
* Amino acid – proteins
* Central Dogma of Molecular Biology
* Dogma, revisited 
* Horizontal transference


[[Media:IT-3B genetic regulation.pdf|'''Genetic regulation''']]
* DNA regulation
* RNA regulation
* Protein regulation
* Global regulatory mechanisms:


[[Media:IT-4B1 Communication with environment.pdf|'''Communication with environment''']]
* Signal transduction
* Signal 
* Receptor
* Transducer
* Actuator
* Examples


[[Media:IT-4B2 Kinetic Chemistry.pdf|'''Kinetic Chemistry''']]
* Definitions
* Law of mass action
* Enzyme-catalyzed reactions
* Hill equation: allosterism
* Hill equation in gene modelling


[[Media:IT-5B (Basic) Laboratory Techniques (in Molecular Biology).pdf|'''(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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<font face="trebuchet ms" style="color:#047DB5" size="3">'''Part 3 Training in Synthetic Biology'''</font><br>
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[[Media:IT-6 Introduction to Synthetic Biology.pdf|'''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 


[[Media:IT-7 standards.pdf|'''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 [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Computer Modelling Practicals] lecture by Vincent Rouilly at Imperial College)


[[Media:IT-9 Synthetic Biology works.pdf|'''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
* Artificial quorum sensing
* Artemisinin production
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