Imperial College/Courses/2010/Synthetic Biology/Computer Modelling Practicals

Welcome

Spring 2010

Instructor: Matthieu Bultelle, Geoff Baldwin.

Room: Biochemistry building, 310.

• This is the OWW page dedicated to the 2010 Synbio Computer Modelling Tutorials
• This page is still a work in progress. It will be complemented as the course progresses.

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
  • Deadline for BioEngineers: 5pm 5th 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)

The first tutorial has two distinct aims:

• Goal 1: help you familiarise yourself with a software called Cell Designer that is popular among Systems and Synthetic Biologists for the simulations of gene-regulatory and biochemical networks.
• Goal 2: provide you with a gentle introduction into the application of the law of mass action to the modelling of biochemical networks

• Part 1: Getting to Know Cell Designer
  • CellDesigner Crash Course (courtesy Dr Vincent Rouilly)
  • Features,GUI,SBML
  • Kinetic Simulations

• Part 2: Build your first models
  • A->B->C
  • Enzymatic Reactions

Practical 2: Gene Expression Modelling (2h)

The second tutorial aims at providing you with the basic tools to model genetic networks, including:

• Standards Model(s) for Constitutive Gene Expression
• Standards Model(s) for Activated and Repressed Gene Expression

Practical 3: Some Synthetic Genetic Circuits(2h)

The final tutorial will introduce you to an interesting synthetic genetic network, and the (wonderful) world of non-linear dynamics