Médiateurs :
François Taddei (Paris Descartes, INSERM), Ariel Lindner (Paris Descartes, INSERM), Stéphane Douady (Paris Diderot), Samuel Bottani (Paris Diderot)
Cet exercice a lieu dès la première semaine de septembre permettant de réfléchir à la notion d'interdisciplinarité en participant à un exercice d'écriture de projets interdisciplinaires par groupe de 4 à 5 élèves. Cette semaine est encadrée par l'équipe pédagogique et quelques tuteurs/ experts impliqués dans l'ED.
Il permet aux étudiants d'acquérir des compétences telles que :
− Etre capable de délimiter une question importante et de définir des approches interdisciplinaires pour l'aborder
− Apprendre à réfléchir plus clairement et à exprimer ses idées.
− Apprendre à critiquer de manière constructive et à accepter la critique.
− Etre capable de discuter ses idées et éventuellement de les rejeter et d'en trouver d'autres. Apprendre à rédiger un projet de recherche
− Avoir des discussions scientifiques soutenues et approfondies.
− Apprendre à interagir en équipe
Les étudiants sont évalués sur le projet écrit et sur la qualité de la présentation orale.
Cours obligatoires pour les étudiants de première année.
Médiateur :
Stéphane Douady (ENS, Paris Diderot)
Aperçu général des systèmes dynamiques, avec petites expériences de démonstrations et exemples d'applications à la biologie. Ce cours s'applique à la fois à donner les outils théoriques de base, à donner des aperçus d'applications particulières, et une vue d'ensemble sur différentes thématiques :
− Notions de non-linéaire (modèle lapin-renard), Dissipatif (pendule), interactions (accrochage d'oscillateurs), chaos, attracteur étrange (de Lorentz)
− Instabilité (de Faraday), équation d'amplitude, dérivation par arguments de symétrie, description générale de l'ensemble des bifurcations
− Exemples de bifurcations classiques (transition de phase), moins classiques (plantes, milieux granulaires) et biologiques (milieux excitables, nerfs)
− Interactions entre modes et motifs spatiaux, chaos spatio-temporel (dualité défauts / ondes). Retours sur la transition vers le chaos (dynamique discrète, scénarios de transition)
− Quelques instabilités morphogénétiques générales (Laplaciennes, de Turing : coquillages, léopard).
Dates : mardis matin 9h30 à 12h, octobre/décembre 2009, à partir du mardi 6/10/2009
Durée : 12*2h30 = 30 heures
Médiateurs :
Michel Morange (ENS), Evelyn Keller-Fox (Harvard)
Ce cours a pour but d'améliorer la capacité des doctorants à mettre les informations scientifiques dans une perspective historique et philosophique à travers l'étude d'exemples fondateurs précis.Ce cours a pour but d'améliorer la capacité des doctorants à mettre les informations scientifiques dans une perspective historique et philosophique à travers l'étude d'exemples fondateurs précis.
Evelyn Fox Keller interviendra sur la thématique « Simplicité - Complexité ».
Pour cela, les doctorants seront encadrés dans la lecture d'articles fondateurs afin d'améliorer leur esprit critique et leur compréhension de la science dans les nombreuses interfaces de la biologie avec les mathématiques, la physique, la chimie et la médecine.
Durée : 2 heures par semaine
Format : cours et débats.
Dates : vendredi matin de 9h à 11h
Début le vendredi 9 octobre, 2e session le 30 octobre.
Dates suivantes sur le Moodle
E.Fox Keller en Novembre 2009
Mediators :
Matthieu Piel (Institut Curie)
Annemiek Cornelissen et Vincent Fleury
General aim:
In this course we propose two theoretical courses and a practical course, aimed at giving examples of what physics can tell about general biological questions, and in particular about the question of how shapes are generated, a process called morphogenesis. The general aim is to show how it is possible to go from a specific biological question develop a quantitative experimental approach and confront data and modeling.
Summary of content:
A first course (3x3h) will be about the physical constraints to Evolution, presented by Vincent Fleury. It is not exactly classical Evo/Devo, but rather a physicist perspective, in the line of Darcy Thomson famous book 'On Growth and Form', on how shapes can evolve, starting with a general introduction on morphogenesis in biology, development and genetics to move towards physical modeling of developing organisms, and concentrate on a few examples, including Evolution of the hand.
A second course (3x3h) will deal with the very important morphogenetic process of angiogenesis (formation of blood vessels), from Physics to pathology. This course will be presented by Annemiek Cornelissen.
The practical course proposed (3x3h) will consist in studying formation of blood vessels during the development of the chick embryo. It required only a simple binocular microscope for observation and an incubator to control the temperature of eggs. The growth pattern of blood vessels can then be extracted and confronted to classical theories for angiogenesis.
The content above is a starting proposal, and the students interested are also welcome to propose additional topics. During the courses researchers from various fields will come to discuss and give seminars. We will also help the students choose and attend interesting meetings at the interface between physics and biology, the number of such meetings being now quite elevated.
Dates : The courses will be of 3 hours each time, between November 2009 and May 2010
The schedule and precise set of courses will be decided after a first meeting, in October 2009, with the student interested to follow the course.
Médiateur :
Minus van Baalen (Laboratoire d'Ecologie - UMR 7625, ENS, Université Pierre et Marie Curie)
Pour Darwin, l'évolution était fermement liée à l'écologie qui l'incorporait. En effet, même s'il n'était pas le 1er biologiste de l'évolution, avec un peu de justification, on pourrait revendiquer qu'il était le 1er écologiste. Malgré cela, l'Evolution et l'Ecologie sont devenues dans le temps des domaines scientifiques complémentaires pratiquement sans interactions.
Les écologistes ont considéré que l'évolution était trop lente pour pouvoir la prendre en compte, tandis que les biologistes considéraient que l'écologie était si rapide qu'ils pourraient sans risque supposer qu'elle était dans un équilibre stable (et l'ignorer). Cependant, dans les années 1950 et 60, la discipline de l'écologie évolutive est née du fait que l'on ne peut pas toujours démêler ces deux processus.
Cette discipline maintenant couvre de nombreux sous domaines : théorie de l'exploitation optimale des ressources, théorie évolutive des traits d'histoire de vie, théorie des jeux, pour n'en citer que certains. Dans les années 90, la théorie de la dynamique adaptative a été développée, pour créer une base théorique solide.
Dans ce cours, Minus van Baalen traitera les aspects de base de la dynamique adaptative (6 heures), et présentera en détail 2 exemples qui montrent comment elle peut être appliquée (Evolution de la Virulence, 6 heures) et ce qui restera un problème ouvert et passionnant (Structure de la population et Evolution de la Communication, 6 heures).
Durée : 18 heures
Dates : 6 demi-journées le lundi de 9h30 à 12h30, à partir du lundi 25 janvier 2010
Mediator : JC Thalabard, MD, PhD (University Paris Descartes & APHP)
Summary
In the land of the monolingual : "Translating a basic finding into a new therapy requires us to speak many languages - scientific, clinical, legal and financial. Yet most of us are hopelessly monolingual, a limitation that substantially slows translational research. Steps have been taken to address this problem, but a lot remains to be done." Nature Medicine 15, 975 (2009) To achieve this goal, in addition to original articles, the major medical journals bring regularly to their readers updates on various aspects of basic research which could potentially be translated to humans. This excursion mainly into major medical journals will help the students; i)to discover their contents, their target readership and how they are structured; ii) to summarize and present the results of both original and review articles.
Program
The following journals will be regularly browsed to form the reading list: Lancet, New England Journal of Medicine, JAMA, Nature Medicine, PLoS Medicine An initial list of articles will be posted in the corresponding section for the course in the M1 moodle web- area. It presently includes the following topics
- Genetic and Molecular Epidemiology
- Infectious diseases
- HIV
- Modelisation of the spread of infectious disease and their prevention
- Systematic Review and Meta-analysis
- Causality
- General Hypotheses
For each session, 1- 2 papers will be selected and read by all the students, who are individualy expected to prepare a written short critical review. A
A group of 2-3 students will be in charge of presenting the selected paper,with an open discussion based on the questions and comments raised by the audience.
Sessions will be held in 2009-2010 on mondays
Mediators : Gregory Batt (INRIA Rocquencourt), Vincent Danos (U. Edinburgh), Vincent Schachter
8 sessions
Basics of numerical simulation and limitations: 1 course-- (Gregory Batt)
Computational aspects of numerical simulation for ODEs, conversion from stochastic to differential rates (including transport), stochastics DEs, Gillespie algorithm. Numerical errors, computational cost of numerical simulation, stiffness, dimensionality, parameter uncertainties and the question of biological significance. Spatially heterogeneous systems, crowding, diffusion limited kinetics.
Boolean and qualitative models: 2 courses, 3TDs (Gregory Batt)
1st TD: (yes, we start with a TD!) modeling and basic analysis of a simple gene network
1st course: Boolean and qualitative models and their dynamics. Thomas' rules.
example "yeast robust cell cycle "http://www.pnas.org/content/101/14/4781.abstract
2nd TD: detailed analysis of a complex gene network (nutritional stress response in E. coli) using GNA
2nd course: computational aspects: search for steady states, formal verification, network inference
3rd TD: connection with experimental data: Saint-Savage et al.
Model building and analysis: 2 courses, 2TDs-- (Gregory Batt)
1st course: notions of sensitivity: local, solution-based and global, sensitivities computation; notions of robustness and computational aspects
1st TD: optimizing genetic circuits by global sensitivity analysis, X.-J. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, and H. Rabitz, Biophys. J., 87(2):2195-2202, 2004. Kitano's paper on a theory of biological robustness. A general computational method for robustness analysis with applications to synthetic gene networks, http://bioinformatics.oxfordjournals.org/cgi/content/full/25/12/i169 Bioinformatics paper
classical papers such as von Dassow et al and Ingolia et al.
2nd course: parameter estimation: identifiability, various optimization-based search methods
2nd TD: benchmarks for identification of ordinary differential equations from time series data, Gennemark and Wedelin, Bioinformatics, 2009; or actual parameter search on a simple but difficult example
Metabolic networks: 3 courses and TDs (Vincent Schachter )
Steady state assumption, admissible flows, decomposition into extreme modes, biomass production rate predictions, analysis, reconstruction
Mediators : Vincent Danos (U. Edinburgh), Gregory Batt (INRIA Rocquencourt), Vincent Schachter
8 sessions
Rules and reactions: 6 courses, 3 TD
1st course: soft introduction to the kappa basics, relation to ordinary reaction networks, refinement of rule sets (qualitative), stochastic vs. deterministic dynamics, reminder on stochastic and deterministic rate constants (units, typical magnitudes, conversion), basics of simulations, refinement of rule sets (quantitative),
TD: trivial circuits to illustrate the basic definitions, small circuits, kinase cascades
2nd course: large scale ppi network dynamics (and percolation), compositional drift
TD: simple allosteric systems, large networks, percolation experiments
3rd course: causality and stories (formal notion of pathway), model reduction
TD: dna processing models (VD + JK,3) 4th course: thermodynamic model of complex assembly, energy functions, positional entropy model, Wegsheider conditions for reactions and rules;
Advanced allosteric models, kinetic traps.
5th course: rule-based molecular dynamics (a la Peter Dittrich, le Novere)
6th course: pde and patterns a la Meinhardt, Kholodenko, Stelling (VD)
Membrane interactions/bigraphs (JK)
Motivations, from rules to bigraphs [1] and bigraphical molecular systems [2,3]representing transport, dynamic compartmentalisation
[1] The Space and Motion of Communicating Agents, Cambridge University Press 2009
[2] Stochastic Bigraphs. Jean Krivine, Robin Milner and Angelo Troina.Proceedings of MFPS XXIV. Vol 218, p73-96, ENTCS 2008.
[3] A Language for the Cell. Troels C. Damgaard, Jean Krivine andVincent Danos. RR-116 ITU Copenhagen. 2009.
MGS and morphogenesis (Antoine Spicher ou Olivier Michel)
Mediators : Ariel Lindner (INSERM/Paris Descartes), Pascal Hersen (CNRS/Paris Diderot)
This course is intended to develop the student's ability to read and critically interpret interdisciplinary papers from impact journals. Through this exercise the students will be exposed to a large spectra of interdisciplinary research domains and methodologies.
This 1st trimester exercise is built of a series of seminars, each prepared by two students from different backgrounds, presenting in detail a research paper of their choice. The underlying hypothesis, background and the results is discussed in detail and the different techniques explained. In addition, the students are asked to suggest further experimental/modeling approaches with respect to their conclusions from the paper at stake.
1. The articles (in PDF format) should be posted no later than a week before the presentation on the secured AIV wiki.
2. All students participating in the course have to fill their comments, including the strong and weak points of the paper as well as points not well understood no later than three days before the presentation.
3. The points raised in the student's feedbacks will be then addressed during the presentation.
4. A Short debriefing of the presenters by the AIV mentors will take place after the seminar
Mediator: Lucy Veisblat (University Paris Diderot), for the department Études Interculturelles de Langues Appliquées (EILA) of the University Paris Diderot
Scientific English (annual course, 48 weeks=72 hours)
Cours d'anglais de différents niveaux (selon tests) ciblés sur l'environnement scientifique; groupes de 10 à 12 étudiants de même niveau, entraînement à la compréhension et à l'expression orales et écrites.
Cours de 1h30, le matin (8h-9h30) ou le soir (18h-19h30)
Enseignement assuré par un intervenant extérieur pratiquant la rédaction ou traduction scientifique
Scientific English (week course, 15h over 5 days)
Stage de préparation à la communication scientifique avec pour objectif spécifique la préparation d'une communication scientifique publique; exercices de déblocage à la prise de parole et à la compréhension orale; utilisation de documents audio, vidéo et ressources en lignes. Situations d'entretiens individuels et par groupes.
Enseignement assuré en alternance par plusieurs enseignants anglophones.
Stage de 15 heures sur 5 jours ; groupe de 5 à 6 participants.
Scientific English : professional communication (week course, 15h over 5 days)
Stage de préparation à la rédaction de documents professionnels en anglais : rapports, courriers, courriers électroniques, supports de présentation. Travail sur l'efficacité de la communication et la concision. Exercices pratiques à partir de documents rédigés par les participants.
Stage de 15 heures sur 5 jours; groupe de 10 à 12 participants.
Enseignement assuré par un intervenant extérieur spécialiste de la communication professionnelle.
General English (annual course, 48 weeks, 96 hours)
Les doctorants souhaitant améliorer leur anglais général ont la possibilité de s'inscrire aux cours de formation continue (niveaux 1 à 5) proposés au public.
• Cours du soir (18h-20h), d'octobre à juin soit 48 semaines
• Stage intensif d'anglais, 30 heures, une semaine en juin
Les doctorants ont également accès en libre-service à l'auto-formation à l'anglais dans les locaux du CRL.
By the department Études Interculturelles de Langues Appliquées (EILA) of the University Paris Diderot
Mediator: Lucy Veisblat (University Paris Descartes)
The department organizes in 2010 two workshops on "French as a foreign Language" open to FDV students focussed on spoken French for professional and academic uses.
Workshop of 30h over 5 days, 15 students maximum. Exercices on oral comprehension and expression, exploration of some aspects of French culture. (session 1: week of January 11th 2010, session 2: week of June 7th 2010.
Mediator: Andrew Murray (Harvard/CRI)
Course Philosophy - What is systems biology?
Our definition is studying how little things come together to produce big things that have interesting properties that none of the little things exhibit in isolation, with an emphasis on understanding the general principles behind these transformations. This includes understanding how a linear chain of amino acids becomes a protein with a specific structure and function, how a group of proteins interact with each other to produce devices for receiving information, processing it, and inducing cellular responses (such as biological clocks), and how the accumulation of mutations leads to the evolution of such sophisticated machines.
The course will use several examples (the Lac operon, decisions in the development of flies and bacteria, clocks, chromosome segregation, evolution, and sex) to explore the existence of general principles that explain the function and evolution of cells and their components. By concentrating on concepts, we hope to make the course accessible both to students from physics and mathematics whose background in biology is weak and to biology students with little exposure to mathematics. The ancestral version of this class included basic instruction in computer programming, but within the format of the AIV/FdV this material will be covered in other classes and you will be encouraged to use these skills to improve your understanding of the material presented in this class.
Duration: 12 sessions of lecture (2h)+discussion(2h)
Mediator: Christophe Zimmer (Pasteur Institute)
Image formation:
Light microscopy: principles and variants
Fluorescence
Point spread function and resolution
Noise
Basic image processing techniques
Image restoration:
denoising
deblurring
registration
Detection:
automatic thresholding
correlation
other methods
Image segmentation:
adaptive thresholding
edge filters
region based methods
Tracking
detection and association
correlation tracking
optical flow
Advanced methods: examples
Inverse deconvolution methods
Deformable models
Statistical detection and estimation
Highlights of image processing in biological research:
Single molecule dynamics
Super-resolution microscopy
Automated phenotyping and lineage tracing
Reconstruction of neuronal circuitry
Duration: 7 sessions of 3h with practice
Mediator: Jean-Luc Lebrun
Course Synopsis
This course is based on the book "Scientific Writing: A Reader and Writer's Guide". It helps identify and articulate the differences between efficient and deficient scientific writing. Through many in-class exercises, it promotes good scientific writing habits such as conciseness and clarity. The course material is mostly provided by the participants: they bring a published or unpublished paper (6 to 8 pages) to the course and learn how to evaluate and improve documents of the same type.
Good scientific writing skills open up many opportunities to the researcher: publications, confrence or seminar attendance. They also lead to better patents, better research partnerships and better funded research. Clarity and efficiency in scientific writing is a testimony to the quality of a researcher; It influences career promotion.
Course structure
- Introduction: "Write to be read" - a reader and reviewer perspective
- Module 1: The 'Why' and the 'How' of each item in a standard scientific paper structure: title, abstract, introduction, body (headings, subheadings, tables and graphs), conclusion
- Module 2: Literature review, role and rules
- Module 3: Elementary principles of composition: reaching clarity, conciseness, precision and fluidity in writing
- Module 4: Identification of writing problems: a walkthrough process to detect structural problems at the sentence, paragraph and paper level
Requirements
• A scientific paper written by the student (not a review) published, submitted, or draft
• Highlighters of various colours
• The companion book: "Scientific Writing: a Reader and Writer's Guide" World Scientific Publishing 2007 will be provided to the participants.
Class size : 20 participants
The trainer
Jean-Luc Lebrun has managed research programs while working at Apple Computer in its Advanced Technology Research group for over ten years. He subsequently invested his energy in the commercialization of research. He teaches scientific writing at the following A-Star* research Institutes: BII, BTI, CMM, DSI, GIS, I2R,IBN, ICES,IHPC,IME, IMRE, SBIC, Simtech, and SSCC as well as medical research centres: SGH, NCCS.
Duration : 2,5 days
Mediator: Konrad Hinsen (CNRS, Synchrotron Soleil)
This series of lectures and exercises provides a practical introduction to using the programming language Python for solving common problems in computational science.
Topics covered (roughly in chronological order):
• Presentation of the Python language and its use in scientific computing
• Basic language features
• Working with files
• Efficient numerical operations (NumPy library)
• Plotting (matplotlb library)
• Moving on to more complex programs: object-oriented programming and error handling
Students are expected to have experience in working with a computer: creating and editing text files, consulting documentation on the Web etc. No prior programming experience is required.
Duration: 6 sessions of 3 hours in the computer room
Mediator: Konrad Hinsen (CNRS, Synchrotron Soleil)
This series of lectures and exercises addresses advanced topics in scientific computing.
Topics covered:
• Basic parallelization using task farming
• Graphical user interfaces (Tk library)
• Managing source code (and more) with a version control system (Mercurial)
• 3D visualization and animation with VPython
Possible additional topics (chosen according to the students' preferences):
• Interfacing C and Fortran code with Python
• Debugging, profiling, optimization
• Performance boosting using Pyrex/Cython
• Handling large data sets (HDF library, Pytables library)
• Advanced visualization using MayaVi
Students are expected to have a working knowledge of the Python language. Some of the additional topics (Interfacing C and Fortran code, Performance boosting using Pyrex/Cython) also require a working knowledge of the C language.
Duration: 5 sessions of 3 hours in the computer room
Mediator: Patrice Denèfle (Ph.D HDR, Qualifié PU (Section 64-65), CEDEP-INSEAD, Senior Advisor, Translational Research and Development, Healthcare Industries, Links Conseil R&D Strategic Committee, MEDICEN)
Scientific careers can be defined as: "Professions in which people carry out or support scientific research or monitoring". This module aims to give science graduates an overview of the real world of science in action and of the diversity of careers open after a master in or a PhD in science.
The course will be organized as a series of talks by science trained professionals at every level, from senior academic or industrial scientists, to patent attorneys, entrepreneurs, company managers and government officials who will present and discuss with the audience their personal story. It will present perspectives from academia in different countries, from industry in large pharmaceutical companies and small start ups, from patents agencies, government agencies etc...The module will also provide an introduction to the relationships between science, innovation and business.
Duration: 12 sessions of 2 hours, start on friday 23 October 2009
Cours d'anglais par internet personnalisés
http://www.gymglish.fr/
GymGlish propose des cours d'anglais innovants et ludiques, fondés sur un moteur d'intelligence artificielle qui délivre chaque jour un email d'activités linguistiques personnalisées en anglais, suivi de corrections.
Mediator: Ivo Sbalzarini (ETH-Zürich)
Duration: 4 full days
The large amount of data generated by modern experimental assays frequently requires computational analysis ("data mining") in order to allow interpretation. At the same time, imaging capabilities have evolved to a point where it becomes possible to study the dynamics of intra-cellular processes in space and time with the help of computational models and simulations. This opens a need for spatio-temporal modeling based on first principles from physics, and the numerical simulation of these models using computers.