La première année du master "Systèmes Complexes" est essentiellement un tronc commun avec le mastère d'Informatique dans lequel quelques modules d'informatique fondamentale sont renforcés. La deuxième année est plus spécifique.

Le M2 est formé par 7 UE d'approfondissement (UEA) de 4ECTS chacune et d'un module "séminaire scientifique" qui rapporte 2 ECTS. La liste des UEA subit des petites variations chaque année pour offrir un panorama le plus vaste et le plus complèt possible.

Voici la liste des UEA ouverte cette année (pointez la souris sur l'intitulé d'un module pour avoir un résumé du contenu) :

- 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 Ren 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.


Le séminaire scientifique consiste à suivre le séminaire "Morgenstern" ainsi que d'autres séminaires organisés par les chercheurs du laboratoire I3S sur des thématiques proches de celles du Master pour un total de 12 séances. La note finale est donnée en fonction de l'assiduité et d'un petite soutenance orale sur l'un des sujets traités pendant les séminaires.