Master IFI - Parcours Systèmes Complexes
Programme des cours 2010/11
Discrete and continuous approaches to model gene regulatory
networks
Lecturers: G. Bernot, J.-P. Comet and
A. Richard
Affiliation: I3S Laboratory, Sophia Antipolis, France.
Abstract: The first part of the course will develop the
basic modelling approach introduced by René Thomas (Brussels).
The space of possible gene expression levels can be decomposed
into several intervals leading to a discrete approach which can
be formalized (according to formal methods of computer
science). We will show how to use formal logic in order to
extract unknown parameter values from the observed behaviours.
We will also explain how some of the current software testing
methods can be used in order to generate interesting "wet
biology" experiments, starting from the formal descriptions of
the interaction graph and the biological hypotheses under
consideration. The second part of the course will develop the
basics of the use of ODE to model gene regulatory networks with
more precise dynamic predictions. For each considered gene, the
production rate is defined as a combination of the various
contributions of the interacting genes and of the degradation
rate. Some examples will be used to illustrate the notions
defined during the course. In particular the simple model of
mucus production in Pseudomonas aeruginosa will be fully
studied. Pseudomonas aeruginosa is a opportunistic bacteria
which infects the lungs of patients of cystic fibrosis.
Neuron Dynamics
Lecturer: B. Cessac
Affiliation: JAD Laboratory, Nice, France.
Abstract: The nervous system is characterized by the
parallel interaction on many sub-systems with scales from
molecules to brain as a whole where, the state of each
subsystem is permanently evolving in space and time.
Understanding these systems requires to develop new
mathematical tools. This lecture is devoted to give skills in
this domain, where both biological and mathematical aspects
will be considered, with the aim of giving a concrete and
operational perspective. The lecture is organised according to
the different characteristic scales in the central nervous
system: Neurons and synapses, neuronal networks and neural
masses.
Natural Computing
Responsable : P. Collard
Affiliation : Laboratoire I3S, Sophia Antipolis, France.
Résumé : L'expression "Natural Computing" est utilisée
en référence à deux démarches scientifiques : soit prendre
inspiration de la nature pour le développement de nouvelles
techniques de résolution de problème soit utiliser un
ordinateur pour synthétiser un phénomène naturel.
Ces systèmes doivent être pensés comme un ensemble d'entités
auto-organisées, adaptatives et distribuées qui reproduisent le
comportement et les schémas organisationnels qui existent dans
les Systèmes Complexes naturels.
L'objectif de ce cours est de présenter au travers d'exemples
(algorithmes évolutionnaires, réseaux de neurones artificiels,
intelligence collective, ... ), le lien entre sciences de la
nature (évolution neo-darwinienne, neurologie, éthologie,
sociologie, ...) et méthodes informatiques.
Algorithms in Structural Biology
Lecturer:
F. Cazals (INRIA-ABS)
Abstract: Understanding the structure-to-function
relationship as well as biomolecular interactions are major
challenges in current structural biology. This course aims at
providing an advanced introduction to the computational tools
which are instrumental in investigating these challenges, in
two directions.
The first part will address current techniques and developments
in practical computational structural biology. Homology
modelling, protein folding, protein and ligand docking,
molecular dynamics techniques will be presented, with an
emphasis on computational methods and algorithms.
The second part, which may be entitled ”Mathematical morphology
for molecular shapes”, will consist of developing the
mathematical tools which are best suited to manipulate Van der
Walls models, with applications to the analysis of the packing
properties of atoms, the description of molecular surfaces and
volumes, and the investigation of voids and cavities. The
classes will revolve around Voronoi diagrams and related
constructions, which offer a unique setting to get exposed to
fundamental mathematical concepts such as Morse theory and
homology calculations, in a combinatorial and algorithmic
setting.
Compute and data grids: Large scale distributed
systems
Lecturer: J. Montagnat
Affiliation: I3S Laboratory, Sophia Antipolis, France.
Abstract: Grids are large scale distributed
infrastructures leveraging on the high performance networks to
federate computing, data and scientific resources from multiple
institutions interconnect through the Internet. Grid
technologies have undergone a very fast evolution these last
years and the infrastructure deployed have become a critical
tool in many scientific disciplines. This lecture describes the
foundation of grids.
It introduces the main computing models exploited with grids to
evolve from cluster computing towards more virtualized
resources and across-institutional user communities. The main
problems encountered when deploying such very large scale
infrastructures are discussed: users identification and
authorization, security of data and computations, heterogeneity
of resources, redundancy and fault tolerance, deployment,
management, and computation flow control... The most wide
spread technologies and their associated middlewares are
reviewed. Several example illustrate the concepts
introduced.
Cryptographie et Sécurité
Responsable : B.
Martin
Affiliation : Laboratoire I3S, Sophia Antipolis, France.
Résumé : Ce cours cherche à illustrer l’utilisation de
la cryptographie pour construire des mécanismes de sécurité.
Après un bref rappel des chiffres à clé secrète et à clé
publique, nous décrirons comment on peut les combiner pour
assurer les principaux services de sécurité : la
confidentialité ; l’intégrité et l’authentification. Nous
illustrerons notre propos au moyen de quelques protocoles
sécurisés parmi les plus courants : Kerberos, SSL, WEP, WPA et
nous en étudierons à la fois la construction et les limites.
Nous nous attacherons autant à l’aspect formel de certaines
attaques sur ces protocoles qu’aux aspects pratiques. Nous
tenterons d’introduire également la notion de sécurité prouvée
qui permet d’analyser formellement le but initial des schémas
cryptographiques : la sécurité. Cette branche récente de la
cryptologie tente de trouver des conditions suffisantes pour
garantir la sécurité. Cette notion sera reprise et approfondie
dans le cours «vérification et sécurité».
Basics in biology and mathématics
Lecturers
(biology): F. Duprat (CNRS, IPMC), F. Brau (CNRS, IPMC), F.
Dayan (CNRS, LJAD), D. Zugaj (Galderma), G. Baudin (CHU Nice)
Lecturers (mathematics): P. E. Jabin (LJAD)
Abstract(biology): This module gives the basics needed
to understand the enormous complexity of a living organism.
Following these courses, students will comprehend the present
and future challenges in designing, performing, analyzing, and
interpreting experimental results in biology. First, the main
concepts that organise life and future directions for research
are exposed. The major components and structures of life are
studied at diverse levels starting from biomolecules (proteins
and others) up to whole organisms (small animals and humans). A
special emphasis is placed on the physiology of some crucial
organs from the nervous and cardiovascular systems, and on
tumors formation in cancer. Second, courses on the experimental
procedures used in clinical, industrial R&D and in
academical research show the numerous needs for advanced
technologies and mathematical modeling of biological systems.
Abstract(mathematics):This module will give the basis
needed to understand the main concepts in computer science and
applied mathematics developed in the Computational Biology
program.
Séminaire scientifique
Le séminaire scientifique
consiste à suivre le séminaire "Morgenstern" ainsi que d'autres
séminaires organisés par les chercheurs du laboratoires I3S sur
des thématiques proches des celles du Master pour un total de
12 séances. La note finale est donnée en fonction de
l'assiduité et de celle d'un petite soutenance orale sur l'un
des sujets traités pendant les séminaires.