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.