Cours FdV

Mentor: Stéphane Douady (CNRS/ University Paris Diderot)

Organization: November 7, 14, 21, 28, Dec 5, 12, 19 ; January: 9, 16, 23 from 14:00 to 18:00
Number of sessions depending on the needs of the participants, until everybody can enjoy life as it should again...
Credits: n*3, with n number of attended sessions (minimum for validation 80% of sessions number)

Synopsis:
If you have a problem with modeling, but never dared to speak openly about it, come and speak with us.
We guaranty anonymity1, and to welcome you with open hearts.
We've all been through that, and we know how hard it can be. We also know how it can be difficult get it out of your chest, and admit it, even to yourself. However we also know how much liberated you will feel after... and we are here to help you... we'll show by our own examples how you can get out of it yourself too, only by yourself ... Yes we are here essentially for you to get comfortable with this issue, and that you can get yourself out of it by yourself !
Anyway, just come and see, we'll be happy to see you.
Cheers !

Mediator: Michel Morange

Dates: First meeting on 02/11 at 9:00 for launch of the course and organization of following sessions with interested participants.

Objective:
Scientists often use scientific or philosophical notions that have different meanings, and a rich and complex history. Some examples: information, entropy, epigenetics, complexity, reductionism, law, contingency. We will work together to characterize these different meanings, and look for what is at stake behind the use (or non-use) of these notions. A particular attention will be paid to notions used differently in different scientific disciplines.

Practical:
1.The first step will be to establish together a list of about twenty notions.
2.Each session will be devoted to the study of one of these notions. It will be prepared by four students who will describe the main meanings and uses of these notions. I will complement by adding some historical information on the introduction of these notions, and the different ways there were successively used. A general discussion will help us to go further in their understanding.

Mentor: Minus van Baalen (Laboratoire « Ecologie & Evolution » UMR 7625 UPMC)

Organization: 4 sessions 22-1, 29-1, 5-2, 19-2 at the CRI 14:00-17:00

Credits: 12 hours

For Darwin, the process of evolution was tightly linked to the ecology that embedded it. Indeed, even if he was not the first evolutionary biologist, with some justification one could claim that he was the first ecologist.
Notwithstanding, the subsequent development was that Evolution and Ecology became complementary and almost non-interacting scientific domains. Ecologists considered that evolution was too slow to take into account while evolutionary biologists considered that ecology was so fast that they could safely assume it was in stable equilibrium (and ignore it).
However, in the 1950s and 60s, awareness grew that one cannot always disentangle the two processes, and the discipline of Evolutionary Ecology was born. This discipline now covers many subtopics: optimal foraging theory, evolutionary life history theory, game theory, to name a few. In the 1990s, the theory of Adaptive Dynamics was developed to put it on a sound theoretical foundation.
In this course I will attempt to cover the basic aspects of Adaptive Dynamics (3 hours) and present in some detail two examples (a bit biased by my own work) that show how it can be applied (the Evolution of Virulence, 3 hours) and what are still exciting open problems (The Emergence of Individuality and the Evolution of Communication). A last meeting (3 hours) can be used to discuss issues and problems that emerged during the previous topics (the entire program is flexible, and we can adapt before if the need emerges).

Mentors: Ariel Lindner (INSERM, Paris Descartes), François Taddei (INSERM, Paris Descartes), Samuel Bottani (University Paris Diderot)
Coordinator: Samuel Bottani

Organization: 13 sessions of 1h on some Fridays late afternoons at the CRI. Dates on the CRI google calendar.
Mandatory presentations for 1st year FdV PhD students.
IF seminars are part of the regular doctoral school scientific life: regular participation of all the FdV PhD students is expected and is not to be deduced for training obligations.

Presentation:
This seminar series aims to provide an overview on a wide scope of interdisciplinary research on issues in Life Sciences, education and research.
Each session by will group 2 short talks (15 minutes) by first year FDV students introducing their research area and subject followed each by a discussion.
The presentation, aimed at a general, but scientific audience, should present the domain's important issues and questions that motivate the students' and their labs' research. These talks should not present research results but provide a good level "popular" understanding of the speaker's domain and the project goals.
Students are assisted for the choice of their title and presentation blurb and are given a personal feedback after their talk.

Mediators : Samuel Bottani, Saskia van der Vies and special guest Melissa McCartney

Mandatory for FDV 1st year students who did not already participate to a critical reading of scientific papers course.

Calendar:
25/10 17:30-19:30: Introduction, guidelines to reviewing
8/11 17:30-19:30: 2 groups presentations
29/11 17:30-19:30: 2 groups presentations
06/12 17:30-19:30: 2 groups presentations
20/12 17:30-19:30: 2 groups presentations

Special sessions with Melissa McCartney:
15/11 15:00-18:00 : Melissa's presentation 1 and 2 groups presentations
16/11 9:00-12:00 : Melissa's presentation 2 and 2 groups presentations

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 articles chosen in interdisciplinary research domains and methodologies.

The course is based on study cases from real publications presented by students after and introduction on guidelines for reviewing articles, Students exercise their critical reading in a series of seminars, each prepared by two/three students from different backgrounds, presenting in detail a research paper of common interest.

Students are asked to critically review both science and writing issues of the publications. The key scientific questions, underlying hypothesis, background and the results are discussed and the different techniques explained. Article features, as title, abstract, paper outline, figures, quality of writing are commented considering how they support the scientific content.

Finally, students are also asked to suggest further experimental/modeling approaches with respect to their conclusions from the paper at stake.

The course will discuss different styles of publication, of journals and the process of scientific publication.

Mentor: Christophe Zimmer (Pasteur Institute) < Cet e-mail est protégé contre les robots collecteurs de mails, votre navigateur doit accepter le Javascript pour le voir >

Organization: 6 sessions of 3h with practice, foreseen start January 2013
Credits: 18h

Synposis:

Image formation principles:
- Light microscopy and fluorescence: principles and variants.
- Point-spread-function and resolution.
- Noise: origins and characteristics.
Basic image processing techniques:
- Image restoration/enhancement: brightness transformations, denoising, correlation and convolution, convolution filters, deblurring, registration, edge filters.
- Image segmentation: thresholding, automatic threshold selection, edge-based methods, region-based methods, correlation matching, watershed transform.
- Time sequence processing: correlation tracking, the association problem, kymograph, optical flow.
- Shape analysis with mathematical morphology: opening, closing, erosion, dilation, structuring element, skeletonization, distance map, gey-scale mathematical morphology, tophat transform, background removal.
Practical image processing with ImageJ:
- Basic features of ImageJ.
- How to program macros.
Advanced image processing:
- Statistical detection and estimation with application to single molecules: Neyman-Pearson detector, ROC curves, Cramer-Rao bound, maximum likelihood estimation.
- Inverse methods for deconvolution.
- Segmentation and tracking by deformable models.
Highlights of image processing in biological research
- Super-resolution localization microscopy.
- Automated phenotyping and lineage tracing.
- Visual proteomics.

In option and will be launched if sufficient students apply to.

Mediator: Konrad Hinsen

Organization: Confirmation of the course: mid-November.

Presentation:
This training is proposed as a combination of an open online course on scientific computing and of an interactive workgroup with meeting sessions. The online course is proposed to provide basic to intermediate training on computer methods for computation, data handling and visualization. Altough this course will be based on scientific python, methods and approaches are valid for other environments. An online forum will provide contacts with course participants around the world and the teacher to share experience on the programming and computing issues they face and to receive mutual support.
In complement to the online course, an interactive workgroup with local meetings at the CRI will allow to cover and discuss the online lessons or specific topics and advanced issues. For start, 4 meetings of 2h (on a monthly based) are proposed, to be extended according to demand. Special work sessions or practicals on given programming and computational techniques will be organized on topics called by sufficient interested people.

External sponsored courses

Cours d'anglais par internet personnalisés / Personalized online English course
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.

GymGlish provides personalized English lessons through daily e-mails. In each lesson, you follow the adventures of the Delavigne Corporation in San Francisco: full of humor, business English, and with a wide variety of accents.

Each morning, you receive an e-mail in English with a variety of written and audio exercises. GymGlish lessons take 10 minutes to complete, and include a story from the Delavigne Corporation, dialogues to listen to, questions to answer, 'mini-lessons', and a personalized revision program.

Once you have sent your answers, you will receive a marked correction e-mail with your score for the day's lesson, personalized explanations, the English vocabulary you have requested to learn more about, the scripts for the audio files, etc.

Mentors: Ariel Lindner (Paris Descartes, INSERM), Samuel Bottani (Paris Diderot), François Taddei (Paris Descartes, INSERM) Pascal Hersen (Paris Diderot, CNRS), Roberto Toro (Pasteur, CNRS), Erwan Bigan (CRI)
Coordinator: Ariel Lindner

Organization: The FdV/AIV workshop, set in Sèvres (near Paris) during 6 days, intends to assemble free spirited students and researchers from broad scientific backgrounds to conceive creative projects at the interface with Life Sciences.
The CIRP workshop attempts to provide the primary basis for collegiality and communication through dialogue and brainstorming on open questions in Life Sciences.
Credits: 5 days (35h)
The workshop is mandatory for Master 2 AIV and first year FdV PhD students.

Aims of the CIRP workshop:
To be able to focus on an important scientific question and to define the means to approach it from different disciplines
To be able to zoom out (have a broader view) and zoom in (be precise and define the key experiments).
To think and express your ideas more clearly.
To gain confidence in your ideas.
To be able to discuss, reject or accept ideas.
To learn to take constructive scientific criticisms.
To learn how to write a research proposal.
To discuss scientific questions thoroughly.
To learn to interact with people from different backgrounds.

The workshop is mandatory for Master 2 AIV and first year FdV PhD students.

CIEP center in Sèvres
CIEP Access / Practical info

Life Science of Naruto ?! A hard rock serious course on Science and Manga !



Life Science of Naruto?! A hard rock serious course on Science and Manga!

Mentor : Stéphane Douady (CNRS/ University Paris Diderot)

Organization: November 5, 12, 19, 26 from 18:00 to 20:00 at the CRI + a special session "Naruto marathon" at a date to be determined.

Credits: 10h

Synopsis:
Apart from having the pleasure to (re)discover Naruto, or to discover at least what everybody around you know and you don't(!), (with the projection of selected episodes), the aim of this module is to use this Manga series to discuss:
The deep signification that we can find in the story and behaviors shown. This part is mostly about cognitive/neuro-sciences and psychology.
The analogies that can be drawn from some aspect of Naruto's world, or how they can be related to "common" biological theories. The idea is to reveal them and then to discuss and challenge them.
The discussion can then go on about the meaning of analogies, their significance and importance, usefulness. Here are some already discovered hints:
Naruto and cognitive sciences: perception and interpretation (with illusions and their mastering), communication and language (and what is actually communicated) and an original (involuntary?) representation of the unconscious brain.
Naruto and psychology: individual freedom, predetermination, social interactions, resilience...
Naruto and Biology: notion of life (vital fluid? what is alive? dead?) the individual, the notion of species, trans-species and bifurcating ones and an (involuntary) and original representation of DNA encoding.
One main practical problem is that it is often hard for someone who has never seen Naruto's story to understand anything from only few episodes. Thus we might want to arrange some "Naruto Marathon" showing in a row a large number of episodes, to give a good overview of the particular world in which Naruto is evolving!

Mediator: Tsvi Tlusty, Princeton Institute for Advanced Studies

Organization: 3 half-days, End of May 2013

Credits: 9h

Synopsis:
Self-reference is a very old idea and an even older myth: Ouroboros, the self-eating serpent, was an icon of ancient religions. Self-reflexivity occurs very naturally when we think or talk about ourselves, for example the first person pronoun "I". It is frequently used in the arts, for example in Don Quixote or in Magritte's painting "ceci n'est pas une pipe". The idea of self-reference is central in the foundations of mathematics, philosophy, linguistics and computation. All these fields are related to the basic liar paradox that we encounter when reading the phrase "this sentence is wrong" and asking whether it is true or false. This paradox lead to Gödel's theorem and to Turing's formulation of computability through the use of recursive functions. The same ideas are linked to self-reproducing machines, and in particular to the molecular machinery of living systems and to the emergence of Life. In the lectures we will review these concepts and relations from various formal and informal angles.
- Lecture 1 - Logic paradoxes and computation (recursive functions, Gödel, Turing, Church).
- Lecture 2 - Self-reproducing machines in technology and Life (von Neumann's machines, origins of life).
- Lecture 3 - Self-reference in language and mind (dictionaries, consciousness etc.)

References:
- Smullyan, Diagonalization and Self-Reference.
- Rogers, Theory of Recursive functions.
- Hofstadter, Gödel, Escher, Bach: an Eternal Golden Braid.
- Nagel & Newman, Gödel's proof.

Mentor: Elisabeth Heseltine (www.communicationinscience.com)

Organization: 3 days 18-20 March 2013 (Max 12 participants, min 6)
Credits: 3 days (21h) Course proposed for validation by the CFDIP

Presentation:
The aim of this workshop is to provide guidance in writing a standard scientific manuscript for submission to a peer-reviewed journal. The structure of other types of scientific communication, such as literature reviews, case reports, conference abstracts and posters, is also covered.

The workshop is limited to 12 participants to ensure discussion. As this is a workshop and not a course, participants are expected to contribute to the discussion at all times.

Participants should be at some stage of writing a draft manuscript to be submitted to a biomedical journal. Three complete drafts will be chosen before the workshop from among those submitted by participants to illustrate the discussion. During the workshop, each section of a manuscript is discussed by the participants after an explanation of the functions of that section. Each day, the participants revise the parts of their manuscripts that have been discussed. A short session covers how to improve writing style. By the end of the workshop, the participants should have their manuscripts ready to send to the journal of their choice! Those participants whose manuscript was not selected are encouraged to send their manuscripts to Ms Heseltine for editing once they have revised them according to what they learnt during the workshop.

Contact with all participants is maintained by e-mail until their manuscript is actually published. This includes revising the manuscripts before submission to the journal, for structure, style and language and revising the accompanying letter to the editor of the journal. Once the manuscript has been returned with reviewers' comments, the revised manuscript are again looked at for clarity, and comments are given on the answers to reviewers' comments and the second letter to the editor of the journal.

Mediator: Antoine Mazières (CRI)

Dates: 24/01 and 31/01 from 18h00 to 20h00

This course aim at presenting a basic initiation to several tools available on the web for free that make the life of a researcher easier. Also, lot of this tools offer "network effects" that allow you to discover what people interested in the same things as you (a paper, a bookmark for example) are interested in.
Some elements of workflow optimization will be covered too (ie. tips and tricks that make your digital life easier):

- Bibliographical tools : Zotero, Mendeley, CiteUlike, Delicious
- Integration of biblio with Word Processing programs : LibreOffice, LaTeX
- Groups frameworks : Googlegroups, googledocs, data sharing
- Quickly building a website, a wiki
- Good usage of bibliographic databases (search operators, histories)
- Advanced usage of pubmed

This is a basic initiation where tools we'll be presented with only a quick overview. The purpose is to help students to choose some tools so they can focus on specific features by themselves, through the extensive existing online documentation.

Coordinator: Evelyne Jardin

Mentors: Barbara Filler (CEO of CCH consulting), Marcelline Bangali (INETOP, Paris, France), Patrice Denèfle (IPSEN), Evelyne Jardin (Careers Consultant, course coordinator)

Organization: dates to be announced.

Credits: 16h Course proposed for validation by the CFDIP

Details of the program:

External sponsored courses

Mediator: Denis LAFEUILLE
http://isefre.org/index.php

Durée : Cycle de base 50 h + en option 50 h en groupes de projet

Dates : Cycle de base : 25 soirées (19 h - 21 h), de Janvier à Octobre 2013, hors vacances scolaires ; le cycle est donc sur l'année calendaire, et non sur l'année universitaire

Description:
Les Cycles DFE constituent un module de formation à l'entrepreneuriat et l'intrapreneuriat. Ils s'adressent à des jeunes désireux d'acquérir une sensibilisation forte au monde entrepreneurial, un contact personnel direct avec des entrepreneurs, et leur permettent de former un réseau avec les anciens des Cycles DFE précédents, répartis dans le monde entier.
Ces Cycles ne concernent chaque année qu'un groupe restreint de participants, de façon à faciliter une forte interactivité avec les différents intervenants. Idéalement, les promotions sont constituées pour moitié par des étudiants français, et pour moitié par des étudiants étrangers, de façon à bénéficier de la richesse qu'apporte une grande diversité.

Ces Cycles comportent trois composantes :
1. des séances hebdomadaires en soirée [19 h - 21 h] (hors vacances scolaires) avec des personnalités ayant vécu dans les années récentes des expériences exemplaires dans le monde de l'entreprise.
2. une journée-visite annuelle ; exemples des dernières années:
- Campus de l'Ecole Polytechnique (Plateau de Saclay) :
- Activités d'Opticsvalley, Filière Entrepreneuriat de l'Institut d'Optique Graduate School, pépinière d'entreprises X-Technologies
- site A380 à Airbus et LAAS (Laboratoire d'Architecture et d'Analyse des Systèmes), tous deux à Toulouse
- salle des marchés de BNP Paribas, puis visite de NYSE Euronext
3. En option : des groupes interdisciplinaires de projet, sur des sujets proposés et encadrés par des entreprises ou organismes, ou proposés par des étudiants du Cycle, porteurs de projet.

Mediators: Matteo Merzagora (TRACES), Richard-Emmanuel Eastes (TRACES)

Dates: 3 days workshop February 26, 27, 28

Objectives:
The main focus will be on oral presentation to a scientific audience. Targeted to phD students it is aimed at providing them with tools and techniques to deliver efficient presentations.

As in all TRACES courses, the seminar will have a very practical approach: more than 2/3 of the time will be spent in practical exercises.

A special attention will be given to horizontal communication, that is, organized exchanges among participants in order to share the individual knowledge and transform it in a shared knowledge.

Details of the program:

Coordinator: Pierre-Yves Bourguignon

Dates: Start October 2012.

Synopsis:
The permanent statistics workshop will provide the students with a frame for discussing topics in statistics, and getting or offering assistance in a mutual teaching spirit.
Under the supervision of the workshop coordinator, the workshop will be mainly animated by motivated students interested in acquiring a broad knowledge of the field, its associated tools, and/or it's applications. A few specialists will be available -though not systematically present- for further discussions of difficulties identified by the students, as well as for organizing short but timely lecture sessions.
A particular effort will be paid so as to capitalize problems, ressources, snippets, etc... in a coherent manner within a wiki-type knowledge base it parallel to an online discussion forum.

Mentor: Roberto Toro, (Génétique humaine et fonctions cognitives URA 2189 Pasteur Institute)

Dates: starting on January 2013 from 9:00 to 11:00 +3 seminars
10/01; 24/01 ; 7/02 ; 21/02 ; 7/03 ; 21/03 ; 4/04 ; 18/04 ; 2/05

Content:
A collaborative introduction to neuroscience and cognitive science, organised around 3 thematic axes: (1) brain evolution and development, (2) neurodynamics, and (3) cognition. These 3 axes will be approached through (1) a study of the literature, (2) seminars, and (3) a concrete, collaborative research project.

Details of the program:

Mediators:
Paolo Pierobon (Institut Curie)
Terence Strick (Institut J. Monod)

Organization: There will be 5 sessions of 2h/week when we will introduce the mathematical and physical basis of stochastic processes. One session will be dedicated to simulation and numerical approaches to stochastic processes. These course will be followed by two sessions of 4 hours when four invited speakers will participate presenting their research in an interactive lecture of two hours.

Dates: 28/03 ; 04/04 ; 18/04 ; 25/04 ; 02/05 from 16h00 to 18h00
16/05 and 23/05 from 14h00 to 18h00

Abstract:
Whether you are dealing with signals, images, cell, bacteria, financial market or simply speaking at the phone with your friend you cannot escape noise! But is that all? Can we learn anything from this noise before trying to get rid of it? In this course we introduce the fundamental concepts of stochastic processes and apply them to physical and biological systems ranging from the molecule to the population. The aim of our course is to give the instruments necessary to understand current research papers in biological physics, system, cell and molecular biology. Four invited speakers will introduce their research subject that will be re-discussed along the course. The course will be organized to be followed by students without a strong mathematical background (but with a strong will to learn something!).

"If you have knowledge, let others light their candles at it." Margaret Fuller

Mediators: CRI staff, Samuel Bottani (Paris Diderot -coordinator)

Presentation:
Mentoring intern students in the lab is an important nurturing process for a PhD candidate, which fosters his growth and development toward full maturity. Mentorship experience contributes to developing essential skills for a PhD graduate as gain of confidence, sense of responsibility and inter-personal communication and coaching skills.
Good mentorship requires personal investment in the task and careful attention to the intern previous experience, studies and motivation. Personal inclination for interpersonal relationships, coaching and scientific motivation helps for success in mentoring. Sensitization and exposure to key steps, different approaches and situations is however important to improve the quality of the intern/mentor relationship and contribute to optimal output and satisfaction for both parties.
The Intern Mentoring Program is proposed in order to promote intern mentoring in the labs by PhD students and to provide support and guidance for them undertaking this task.
In agreement with their supervisors (and probably under their formal authority) interested FdV students are invited to take responsibility of an intern in their lab for a duration of their choice. Participants should contribute to a discussion group and an half a day workshop on teaching, coaching and mentoring interns organized later in the year to address any issue that arises and debrief in common on the experience. Involved FdV students are credited for 2 days training obligations.