78 lines
3.7 KiB
Org Mode
78 lines
3.7 KiB
Org Mode
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#+TITLE: Petri Nets for Biomodelling: An Introduction
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#+LANGUAGE: en
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#+ATTR_HTML: :alt in French :class lang-lifted
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[[file:../fr/pn-biomodelling.org][file:../content/imgs/fr.png]]
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#+ATTR_HTML: :alt return home :class home
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[[file:home.org][file:../content/imgs/home.png]]
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The goal of this course is to introduce students to [[https://en.wikipedia.org/wiki/Petri_net][Petri nets]],
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explore some of their properties, and show how Petri nets can be used
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in biomodelling. After having taken this course, the students will be
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able to build Petri net models of biological phenomena (including
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using some extensions, like basic coloured Petri nets and inhibitors
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arcs) and to relate the formal properties of these models to the
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biological properties of the modelled phenomenon.
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This course does not require prior experience in theoretical computer
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science or biology and is part of the course "Network medicine" taught
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to students following the [[https://www.universite-paris-saclay.fr/fr/education/master/m2-genomics-informatics-and-mathematics-for-health-and-environment-geniomhe#presentation-m2][GENIOMHE]] MSc. program at [[http://www.univ-evry.fr/fr/index.html][Université
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d'Évry]].
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The course consists of 4 sections, the first three focusing on Petri
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nets and their properties and the last one being a practical
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assignment. The sections are designed to reflect logical differences
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in content and need not correspond to actual sessions.
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#+ATTR_HTML: :alt image of Creative Commons Attribution Alone licence :class ccby
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[[https://en.wikipedia.org/wiki/Creative_Commons_license][file:../content/imgs/ccby.png]]
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The materials of this course are distributed under the [[https://en.wikipedia.org/wiki/Creative_Commons_license][Creative
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Commons Attribution Alone licence]].
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* Definitions
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This section starts by motivating the model of Petri nets and gives
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the definition of the model and of the evolution modes. Particular
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focus is on the synchronous and the asynchronous evolution
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modes. The parallel with [[https://en.wikipedia.org/wiki/Multiset][multiset]] rewriting is also shown.
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The slides for this section are available [[file:../content/courses/pn-biomodelling/network-medicine-4.pdf][here]].
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* Extensions
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This sections briefly points some limitations of the original Petri
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net model and shows the classical extended variants, like coloured
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tokens or inhibitor arcs. The cost of extensions is intuitively
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evaluated with respect to decidability: more expressive variants are
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often undecidable.
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The slides for this section are available [[file:../content/courses/pn-biomodelling/network-medicine-5.pdf][here]].
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* Properties
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In this section some of the fundamental structural and behavioural
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properties of Petri nets are presented. Behavioural properties are
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introduced before structural properties because the former are
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easier to grasp. This section includes a number of exercises to be
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done interactively with the students. Additional exercises may be
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given on the whiteboard.
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The slides for this section are available [[file:../content/courses/pn-biomodelling/network-medicine-6.pdf][here]].
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* Case Studies
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This section is a practical assignment in which the students should
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use Petri nets to model and analyse two simplified biological
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networks. [[http://projects.laas.fr/tina/][The TINA toolbox]] is the suggested tool for Petri net
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analysis, even though other tools may also be used.
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The text of this assignment is [[file:../content/courses/pn-biomodelling/network-medicine-pn.pdf][here]].
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* Local Variables :noexport:
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# Local Variables:
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# org-link-file-path-type: relative
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# eval: (auto-fill-mode)
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# ispell-local-dictionary: "en"
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# End:
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