Assignment 2: Modelling in BioPEPA

The second coursework assignment is now out, and due on Thursday 25 March, three weeks from now.

The assignment involves modelling a small signalling pathway using the BioPEPA language. Lecture 14, on Thursday 11 March, will include an introduction to BioPEPA; and Stephen Gilmore will give a guest lecture presenting the Eclipse plugin for BioPEPA on Monday 15 March.

The exercise is fairly open-ended, and you should feel free to modify it and follow your own investigations as you find appropriate. If you have find (or solve) any particular difficulties, especially with the modelling tools or other technical issues, please post comments below.

Links: Assignment 2; BioPEPA; The BioPEPA Eclipse plugin.

2 Responses to Assignment 2: Modelling in BioPEPA

  1. Chris B says:

    Do you think that this seminar might be useful for MLCSB students?

    From the PEPA club mailing list:

    Dear all,

    PEPA club will be meeting as usual this Friday at 11am in room 3.02 of the Informatics Forum.

    This week the speaker will be Maria Luisa Guerriero. Title and abstract below.

    Maria Luisa

    Title: Complementary approaches to understanding the plant circadian clock

    I will describe a Bio-PEPA model of the Ostreococcus tauri clock. We exploit the different analysis methods offered by Bio-PEPA to show how multiple approaches lead to a more complete understanding of the clock. We first investigate the difference between the continuous-deterministic and the discrete-stochastic representations of the model. Then, focusing on stochastic methods, we use show stochastic simulation and model-checking results which allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. We also use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness.

    This is a joint work with Ozgur Akman, Laurence Loewe and Carl Troein and will be presented at FBTC 2010.
    pepa-club mailing list

  2. ianstark says:

    Yes, I do. I had already mailed the speaker about this — it looks interesting and relevant. PEPA club has lots of this kind of thing, and it’s good.