Modelling and analysing MAPK signalling pathways

These materials have been developed in collaboration with Professor Monika Heiner and her team at the Computer Science Department, Brandenburg University of Technology, Cottbus, Germany.

The lecture is delivered by David Gilbert, with the help of Luis Arenas, from the Synthetic Biology theme in the Institute of Environment, Health and Societies at Brunel University.

Abstract

Prior knowledge required: Suitable for biochemists with an understanding of enzyme kinetics.

Lecture

In this lecture we will show how to model signal transduction pathways.

Specifically, we will teach you how biochemical networks can be modelled a qualitative approach -- Qualitative Petri nets, and quantitative approaches -- Continuous Petri nets and Stochastic Petri nets. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building.

We will illustrate our approach using a generic model of a signalling cascade, and then relate this to existing models of the MAPK pathway, e.g. Levchenko, Brown and Schoerbel. We will show how the dynamic behaviour of such a pathway is related to its modular structure.

Finally, we will describe the latest developments in the applications of modelling and `crystal ball' gaze how these might be important for you to know about in your careers.

Practical

There will be a practical part of the lecture where you will learn how to construct, modify and explore the behaviour of some simple models in Petri nets using the suite of Snoopy and related tools, from the Brandenburg University of Technology Cottbus.

Materials

• Reading list here

• Slides MAPK modelling, Quorum Sensing Modelling.

• Exercise

• Snoopy software
  • Locally: \\uxisapp1\apps\Snoopy\snoopy.exe
  • From the Snoopy website

• Models

  All models:

  • \\uxisapp1\apps\Snoopy\Examples
    or from here:-
  • zip file of snoopy models

  Or as expanded files:

  • Simple a->b
  • Simple H2O
  • Enzymatic reaction
  • MAPK general model
  • MAPK - Levchenko
  • MAPK - Kholodenko (oscillating)
  • RKIP

The Centre for Systems and Synthetic Biology at Brunel University in London, UK is strengthening its activities in Bioinformatics, Systems Biology and Synthetic Biology.
There are several open positions for talented and able academics, postdoctoral researchers and PhD students in the area of Systems and Synthetic Biology at Brunel.
For more details, contact Professor David Gilbert or Professor Nigel Saunders.