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Abstraction, Modularity and Compositionality
in Genetic and Proteic Networks
ACI VICANNE
IHP, Paris 23-24 January 2006
ARC MOCA
http://contraintes.inria.fr/moca
François Fages
IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
François Fages
IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
depends on our choice of observables.
François Fages
IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
depends on our choice of observables.
François Fages
IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
depends on our choice of observables.
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François Fages
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IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
depends on our choice of observables.
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François Fages
1
IHP Paris, Jan 2006
Transposing Computer Science Notions
to Systems Biology
Formally, “the” behavior of a system…
depends on our choice of observables.
Behavior in
different/all initial conditions
or in different/all contexts
François Fages
IHP Paris, Jan 2006
Theory of Abstract Interpretation
abstraction
Boolean models
Discrete models
Differential models
Stochastic models
François Fages
IHP Paris, Jan 2006
Query: Set of Stationary States ?
abstraction
Boolean analysis
abstraction
Boolean models
abstraction
Discrete models
abstraction
Differential models abstraction
Stochastic models
François Fages
Discrete analysis
Differential analysis
Stochastic analysis
Issue of
correctness / optimality
of an abstraction
w.r.t. a query
IHP Paris, Jan 2006
Modularity and Compositionality
When the behavior of a complex system is a function of the
behavior of its components…
François Fages
IHP Paris, Jan 2006
Modularity and Compositionality
When the behavior of a complex system is a function of the
behavior of its components…
Notion relative to « behaviors » hence to our choices of observables
for the complex system and for the components.
François Fages
IHP Paris, Jan 2006
Modularity and Compositionality
When the behavior of a complex system is a function of the
behavior of its components…
Notion relative to « behaviors » hence to our choices of observables
for the complex system and for the components.
Complex systems may be modular for some observables, and not
for other choices.
François Fages
IHP Paris, Jan 2006
Modularity and Compositionality
When the behavior of a complex system is a function of the
behavior of its components…
Notion relative to « behaviors » hence to our choices of observables
for the complex system and for the components.
Complex systems may be modular for some observables, and not
for other choices.
Mathematically, any system can be made modular by considering
the behaviors of its components in all contexts.
François Fages
IHP Paris, Jan 2006
Overview of Talks
Abstraction
M. Kaufman. Logical and differential approaches to p53-mdm2 net
V. Danos. A model’s model
Modularity
B. Novak. Eukariotic cell cycle: modules and mathematical models
A. Siegel. Analysis of ODEs by decomposition into modules
Compositionality
R. Blossey. A compositional approach to regulation networks
F. Tarissan. Analysis and synthesis of self-organizational systems
V. Hakim. Structure of small gene networks and evolution in silico
François Fages
IHP Paris, Jan 2006