ER 06 (2011) : Rule-based modeling and application to biomolecular networks

Du 14 au 18 février 2011 — ENS Lyon

Links to main documents

Objectifs

The goal of this course is to give an overview on rule-based modelling.

Rule-based approaches (as in our own Kappa, or BNGL, or many other
propositions allowing the consideration of « reaction classes ») offer
some means to capture combinatorial molecular interactions as we find
them in biological subcellular systems. This is trying to fill a need
that seems ever more pressing – as molecular biology uncovers more
amazing combinational structures. In so doing we get a more physically
realistic, less parameter-hungry, and more structured approach to the
modeling/programming of combinatorial molecular networks.

We will explain the approach through numerous motivating examples. We
will also reenact various methods commonly employed in the
verification and analysis of concurrent systems to support our
approach with analytic tools, such as: static analysis (qualitative
and quantitative) for reachability questions and for the reduction of
dynamical systems, causality analysis (including methods for the
compression of partial time traces), and more specific « termination »
methods using local energy functionals to guarantee thermodynamical
correctness.

The intended audience is students and staff in theoretical computer
science/concurrency theory, computational biologists with an interest
in modelling techniques, statistical physicists/applied mathematicians
with an interest in biomodelling.

Intervenants

  1. Vincent Danos
  2. Jérôme Feret
  3. Jean Krivine
  4. Gregory Batt
  5. Jonathan Hayman

Le matériel pédagogique sera en anglais.

Les cours auront lieu en anglais.

Timetable

Monday 14th [Amphi B]
  • 9h30: Welcome [Amphi B, 3rd floor]
  • 10h00-12h00: Basics of modeling (V. Danos) [Amphi D, ground floor]
     
  • 14h00-15h30: Basics of modeling (V. Danos) [Amphi B]
  • 15h45-17h00: Basics of modeling (V. Danos) [Amphi B]
Tuesday 15th [Amphi B]
  • 10h00-12h00: Introduction to kappa (J. Krivine)
     
  • 14h00-15h30: Dynamics (J. Krivine)
  • 15h45-17h00: Dynamics (J. Krivine)
Wednesday 16th [Amphi B]
  • 10h00-12h00: Static analysis (J. Feret)
     
  • 14h00-15h30: Model reduction (J. Feret)
  • 15h45-17h00: Model reduction (J. Feret)
Thursday 17th [Amphi B]
  • 10h00-12h00: Model reduction (J. Feret)
     
  • 14h00-15h30: Modeling session: epigenetics (J. Krivine)
  • 15h45-17h00: Modeling session: epigenetics (J. Krivine)
Friday 18th [Amphi B]
  • 10h00-12h00: Energy and syntax (V. Danos)
     
  • 13h15-14h00: evaluation for ENS students
     
  • 14h00-15h30: Extensions (G. Batt)
  • 15h45-17h00: Extensions (J. Hayman)

Content

Basics of modeling : Petri-Nets, mass action law, detection of equilibriums and steady states, thermodynamic limit (Kurz theorem).

Introduction to kappa : Notion of model in biology, syntax and operational semantics.

Dynamics : Gillespie’s algorithm, scalability issue, causality.

Static analysis : Qualitative analysis, reachability (completeness result), species enumeration algorithm.

Model reduction : Information flow, ODE semantics, stochastic semantics.

Energy and syntax : Information flow, ODE semantics, stochastic semantics.

Extensions : Compartments, agent variants,diffusion.

Logiciels

Pré-requis

Ce cours ne nécessite pas de connaissances préalables.

Les notions fondamentales utilisées seront toutes introduites pendant le cours.

Bibliographie

Correspondant local

Olivier Laurent

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