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.

Regards,

Maria Luisa

Title: Complementary approaches to understanding the plant circadian clock

Abstract:

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.

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http://dx.doi.org.ezproxy.webfeat.lib.ed.ac.uk/10.1146/annurev.physchem.58.032806.104637

]]>I’m not sure how well this would translate to drawing Petri Nets, but I imagine it would do a pretty good job. You just need to specify two different kind of node (circles and boxes for places and transitions).

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