Imperial College/Courses/2009/Synthetic Biology/Computer Modelling Practicals

Welcome
Spring 2009

Instructor: Matthieu Bultelle, Geoff Baldwin.

Room:     Biochemistry building, 310.


 * This is the OWW page dedicated to the 2009 Synbio Computer Modelling Tutorials
 * This page is still a work in progress. It will be complemented as the course progresses.
 * Please come back often!

Regarding the Coursework

 * The practical details are still to be finalised but you can expect the following
 * One piece of coursework is to be handed in to your departmental secretary
 * Departmental rules regarding deadlines will apply
 * A paper and an electronic version are to be submitted
 * Deadline for BioEngineers: 5pm 6th Feb


 * We expect you to submit a coursework that is clear,concise and well presented. Here are a few tips:
 * Reply to the questions in order
 * Indicate clearly what question you reply to
 * Indicate clearly what your answer is.
 * Do not forget to label your simulations...
 * Please keep your answers short
 * But not too short of course: you still have to detail your reasoning and how you have come up to your answer
 * Your coursework should be written in English.
 * This may sound obvious but it means it should be easy to read
 * This also means that equations are a means to an end! Use them to support your argumentation but do not forget to explain what they mean.
 * Relevant simulations should be included and commented.

=Computer Lab Overview=

Practical 1: Introduction (2h)

 * Short Presentation: "All the models are wrong, but some of them are useful", George Box.
 * Short Presentation: CellDesigner Crash Course  (Thank you vincent)
 * Features and GUI
 * Kinetic Simulations
 * SBML
 * Hands-on: Build your first kinetic models.

Practical 2: Enzymatic Reactions(2h)

 * Description and Simulation of a standard Enzymatic reaction
 * The Steady State Approximation

Practical 3: Gene Expression Modelling (2h)

 * Constitutive Gene Expression
 * Activated and Repressed Gene Expression
 * Mystery Circuit


 * 30th January:  It has been brought to my attention that the questions regarding the reressilator were not explicit enough. I have therefore changed them a bit. Hope it is better now
 * March the 9th: I would like to remind the life-scientists that for them the section on the mystery circuit is not compulsory for their coursework. However, I strongly advise them to have a look at it as it is very useful for the rest of the course.