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

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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.