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

Design Practical: Introduction to Design(2h)

This extra session aims at giving you an insight into the design of (simple) synthetic pathways. The material presented in this session is not part of the coursework but should prove useful for your mini-iGEM project.