Comments for Models and Languages for Computational Systems Biology http://blog.inf.ed.ac.uk/mlcsb Wed, 10 Mar 2010 12:29:00 +0000 hourly 1 http://wordpress.org/?v=3.4.2 Comment on Assignment 2: Modelling in BioPEPA by ianstark http://blog.inf.ed.ac.uk/mlcsb/2010/03/assignment-2-modelling-in-biopepa/comment-page-1/#comment-10 ianstark Wed, 10 Mar 2010 12:29:00 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=209#comment-10 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. 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.

]]> Comment on Assignment 2: Modelling in BioPEPA by Chris B http://blog.inf.ed.ac.uk/mlcsb/2010/03/assignment-2-modelling-in-biopepa/comment-page-1/#comment-9 Chris B Wed, 10 Mar 2010 12:21:49 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=209#comment-9 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. 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. _______________________________________________ pepa-club mailing list pepa-club@inf.ed.ac.uk http://lists.inf.ed.ac.uk/mailman/listinfo/pepa-club 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.

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.
_______________________________________________
pepa-club mailing list
pepa-club@inf.ed.ac.uk
http://lists.inf.ed.ac.uk/mailman/listinfo/pepa-club

]]> Comment on Lecture 13: More Stochastic Kinetics by ianstark http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-13-more-stochastic/comment-page-1/#comment-8 ianstark Mon, 08 Mar 2010 17:45:26 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=203#comment-8 Thanks, I've fixed that up now. Thanks, I’ve fixed that up now.

]]> Comment on Lecture 13: More Stochastic Kinetics by s9269200 http://blog.inf.ed.ac.uk/mlcsb/2010/03/lecture-13-more-stochastic/comment-page-1/#comment-7 s9269200 Mon, 08 Mar 2010 13:20:25 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=203#comment-7 The hyperlink for 'Stochastic Simulation of Chemical Kinetics' is broken. The correct one is: http://dx.doi.org.ezproxy.webfeat.lib.ed.ac.uk/10.1146/annurev.physchem.58.032806.104637 The hyperlink for ‘Stochastic Simulation of Chemical Kinetics’ is broken. The correct one is:

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

]]> Comment on Typesetting Petri Nets by Chris B http://blog.inf.ed.ac.uk/mlcsb/2010/02/typesetting-petri-nets/comment-page-1/#comment-6 Chris B Fri, 19 Feb 2010 12:27:17 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=171#comment-6 I've found dot2tex to be very useful for automata and other LTSs in the past. Though, again, it's difficult to get it to adjust the layout to anything other than that which it chooses... It does pretty well at the layout until you start drawing /really/ complicated stuff though. You can choose the graph layout algorithm that it uses which gives a bit of flexibility. 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). I’ve found dot2tex to be very useful for automata and other LTSs in the past. Though, again, it’s difficult to get it to adjust the layout to anything other than that which it chooses… It does pretty well at the layout until you start drawing /really/ complicated stuff though. You can choose the graph layout algorithm that it uses which gives a bit of flexibility.

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).

]]> Comment on Lecture 8: Mix, match and use temporal logics by ianstark http://blog.inf.ed.ac.uk/mlcsb/2010/02/lecture-8-mix-match-and-use-temporal-logics/comment-page-1/#comment-4 ianstark Tue, 09 Feb 2010 18:32:13 +0000 http://blog.inf.ed.ac.uk/mlcsb/?p=124#comment-4 We have comment spam! How flattering. I've deleted the self-promoting URL though. We have comment spam! How flattering. I’ve deleted the self-promoting URL though.

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