Master AIRE 2014

Master AIREApproches Interdisciplinaires de la Recherche et de l’Education

2014-2015

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Master AIRE

Centre de Recherche Interdisciplinaire8-10 rue Charles V

75004, Paris.

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Dear AIRE Students,

We first wish to welcome you to our master program. Together, we’ll make sure that you spend an exciting time at the Center of Interdisciplinary Research in Paris.

By the time you’ll be given this short guide, you’ll have already started the year and met your fellow students. This guide will sum-marize most of the courses and opportunities offered by our pro-gram. Its goal is to help you best enjoy and use the time that you will spend with us.

The AIRE Team.

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Contents

General Information 7

1. M1 / AI 111.1 General Information 111.2 The content of the first year (M1) 111.3 Planning of the Year 131.4 Details of the Courses 141.5 Who to Contact ? 251.6 What’s next ? 26

2. M2/AIV 272.1 Content & Planning of the year 272.2 Details of the course 272.3 Who to contact ? 32

3. FOSTER/M1 353.1 General Information 373.2 The content of the first year (M1) 373.3 Planning of the Year (2014-2015) 393.4 Details of the Courses 393.5 Who to contact? 42

4. FOSTER/M2 434.1 Content & Planning of the year 434.2 Details of the course 434.3 Who to contact ? 44

5. INTERNSHIPS 45

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The AIRE Master is designed to help you find your way in research and design your professional carreer in science and education. You will have the opportunity to learn what research is, to get a lot of practical experience in labs and companies, to meet with many researchers and to discuss recent interdisicplinary research articles and reviews. At the end of the master, some of you will apply to a PhD program, in France or abroad. Others will start their own project, startups, or join a private com-pany in the fields of science and higher education. One of our role as teachers is to guide you into this process.

We encourage creativity, original projects and ideas. So, do not hesitate to interact with us, with the other students, to participate to extra curriculum activities such as the CRI scientific clubs. You can also organize events, create or participate to scien-tific clubs, invite researchers, etc... Be involved, share your knowledge and expertise and you will spend a very fruitful year with us.

There are many different ways to benefit from the master program, and many dif-ferent ways to teach and learn. You will probably meet other fellow students with radicaly different background than you. The idea is for you to share you knowledge, to discuss about science, to confront your ideas, either during the fridays sessions or during the clubs. Be creative, don’t be shy and try new things, or new projects. If you need help, come to us and we’ll try to guide you as best as we can.

There is a lot of diversity in this master, but for this to work we have to share several common values and adopt a few rules. Let’s list them.

1 - Discussions should remain at all time argumentative and, needless to say polite. The important point here is that it is not usefull to say that you disagree with one idea. What’s usefull is to explain why you disagree and if possible to propose your own reflexion and idea on the topic.

2 - Be proactive in class. There’s no point for you to attend the classes if you do not try to participate to the discussion. We know it’s difficult to ask questions, but it is worth trying again and again. As a rule of thumb, if you don’t understand something, just ask !

3 - Come prepared. Read the, course materials, the article or the reviews several times before the classes. Participate to the Moodle, engage in discussion before and during the sessions.

3 - Be on time and respect deadlines. You have to arrive on time in class and meet the deadlines given by the teachers. If you think you cannot attend a class and/or meet a particular deadline, let us know as soon as possible, we may find a solution. If you don’t let us know, we will have to take your absences into account in your

General Information

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evaluation.

4 - As you will quickly observe, the M2 teachers are very, very busy. We devote a lot of time to organize and coordinate the master. But, as all researchers, we also have to manage our labs, devote some time to our PhDs etc... For this reason, it is not possible for us to be available 24/7. Unless you have a urgent matter to discuss with us we’ll prefer to meet with you before or after the Fridays sessions. Send us an email or stop by to make an appointment.

5 - Respect the work of your fellow students. At several occasion you will have a choice between finishing your experiments in your internship lab (or your own personal project, clubs, etc...) and attending a class or a presentation made by your co-students. The priority should be given to the Master. At all times. It’s up to you to organize your schedule so that all fridays afternoon are free. During internships defense, you are all expected to attend at all time, and not only for your talk, which is very disrespectful for your colleagues.

Also and importantly, we encourage creativity. You can organize events, create or par-ticipate to scientific clubs, invite researchers to attend to the friday sessions or give a talk, etc... Be involved, share your knowledge and you will spend a very interesting, rich and entertaining year with us.

APPROCHES INTERDISCIPLINAIRES DU VIVANT

INTERDISCIPLINARY APPROACHES TO LIFE SCIENCES

AIV

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1. M1 / AI

1.1 General Information The first year of the Master is designed to teach primarily synthetic and systems bio-logy. You will also be trained in computer science, statistics, experimental methods, biophysics and more generally on quantitative approaches in life sciences. Each AIV year class brings it’s novel mix of biologists, computer scientists, physicists and engi-neers. This diversity in academic paths is an exceptional opportunity for you to disco-ver the power and efficiency of collaborative and mutual teaching and learning.

We expect you to invest a lot of your skills and energy in the different courses. This means to prepare all courses, in particular by reading science articles, to ask questions when you don’t understand something and to be proactive in classes. You are pro-bably already registered to our online teaching platform called Moodle. This is a very powerful tool and you’ll have to use it for practically every course. Teaching materials (articles, PDFs) will be posted by the teachers for you to read and think on before the courses. You will also have to exchange using the dedicated forums in the Moodle. It’s therefore important for you to be at ease with this tool as soon as possible. Note that you’ll also be evaluated on how much you participated to the Moodle for the various courses.

The spirit of the Master is to responsabilize the students and to maximize exchanges amongst them. As a result it is crucial that you attend all courses. Students are also expected to be on time and to respect deadlines. If you cannot come to a course, let the teachers know about it beforehand. Similarly, if you feel that you are not going to be able to meet a deadline, or if you have a problem with a course, do let us know as soon as possible. It’s much easier to find a solution if we are aware of the problem in advance.

1.2 The content of the first year (M1)

• First Semester (September - January)

The first semester starts by a 3 weeks long bootcamp that gives a condensed overview of the biology, chemistry, math and physics that you will see during the semester. Since you all come from different scientific background we try to give a feeling of the subjects that will emerge during the semester, and to give an intuition on which subjects the students should start working on their own. Typically, a student with physics background needs to work on fundamental biological concepts such as cen-tral dogma, evolution, DNA, methods in biology, while a biologist usually needs to

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focus more on the mathematical and physical concepts that are used in quantitative description of living systems.

After this bootcamp, several core courses will take place every week. You will learn the theoretical and practical concepts that are required to perform scientific research at the frontier between biology, math and physics.

UE1 --- Science and medicine (7 sessions, J-C. Thalabard)UE2 --- Systems Biology (12 Sessions, C. Nizak)UE3 --- Synthetic Biology (12 Sessions, J. Wintermute)UE4a --Computational Biology I (12 Sessions, G. Batt)UE4b --Computational Biology II (8 Session, R. Harmer)UE5 --- Statistics (12 Sessions)UE6 --- Dynamics of living systems (8 Sessions, E. Farge & T. Betz)UE7 --- Introduction to quantitative biology (Lab: 6 Days, M. Piel, Course: 4 sessions N. Minc , G. Romet-Lemonne)

You need to validate 6 courses, meaning to have a final grade equal or larger than 10/20. Grades will be based on your attendance, oral participation in classes, quality of your homework and success to the final exam. Although you need to validate 6 courses over the 8 that are proposed, we do expect you to follow all courses and pass all exams. For your final grades, we will keep the 6 best ones.

Regarding the grades, please do note that, by definition their meaning is very limited - what does that really mean to have 14/20 to an exam? How much does that tell about your skills and deep understanding of a scientific domain? This is why we will also provide you with a written evaluation, detailing what are your strong skills and in which aspects you should improve for each courses. We will also provide you with mid-term oral evaluation through an informal and interactive discussion between the master organizers and the M1 student.

During the first semester, you will have regular possibilities to interact with tea-chers. For this we have implemented 2 sessions per month where either Timo Betz (Monday morning), or Pascal Hersen (Friday morning) will offer time to help you in scientific and academic problems. Please check the schedule for the dates and contact the teachers at least 3 days before the sessions with possible questions you have.

Furthermore, we have implemented a mid-term exam, where each student will have 30 minutes to present his/her knowledge on the predefined subject of Michaelis Menten enzyme kinetics. Students are expected to present in a short 10-15 chalk-talk the basic concept and the mathematical modelling. Then you will discuss for 15 minutes general questions regarding the subject. This is an important step and students should be well prepared. In case of insufficient knowledge, students will have to follow extra coursework to ensure best results in all the classes.

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• Second Semester (February - July)

The second semester will focus on practicing research. You will spend at least 5 months in a research lab. You will also have some mandatory events at the CRI :

UE2.1 --- Seminars (Interdisciplinary Fridays)UE2.2 --- Scientific Communication (9 sessions, Matteo Merzagora)

Both classes will be evaluated based on your attendance, oral participation and ori-ginal contributions.

• Research Internship (February - June)

The research internship is an integral part of your training. The internship will be full time, and should ideally consist in a defined project that will lead to results within the 5 month period. Ideally the internship runs from the beginning of February to the end of June, but this can be subject to individual changes as long as the internship lasts at least 5 month. Any research projects related to synthetic, systems and quanti-tative biology are possible. It is a great opportunity for you to discover what it actually means to do research in a laboratory. See the details on how to find an internship at the end of this booklet.

• iGEM competition

As an alternative to this long internship, you can apply to the iGEM AIV Team. Every year a small group of students from AIV and other Masters programs around Paris gather their strengths and are hosted by the CRI to setup an iGEM project and participate to this competition of synthetic biology. This usually starts by brains-torming sessions and project building and does not require a full time involvement before may or June. Meanwhile we expect that you find an internship of typically 3 to 4 month before joining the iGEM Team. Note that since the iGEM competition finale takes place in November, you will have to organize yourself to stay in the team up to that date. For those of you continuing with us in the second year of the Master, this means that your first lab rotation of M2 will be dedicated to finishing the iGEM team project.

1.3 Planning of the YearYou can consult the year agenda on the website. Some of the dates may change so do not hesitate to ask your teachers. Here is a list of important dates for the M1 AIV.

• Bootcamp - starting on the 1st of september. • Opening days - 1-2 october (to be confirmed)• Informal feedback session I - around 23/10. TBA• MIDTERM EXAM: Oral exam about Michaelis Menten kinetics - beginning of

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• Deadline for internship «convention de stage» - 15/12.• First semester exams - 17/12 (Exp methods); 15/12 (DynLivSyst, presentation);

12/12 (Statistics); 05/01- 9/9 (ComputBio + Synthetic Bio, Systems Bio).• Informal feedback session II - around 24/01. TBA• Start of the internship - 3rd of February.• Informal feedback session III - around 16/05. TBA.• Internship defense - early July 2013.• Debriefing - After Internship defense session• Internship defense - 07 of July 2013.

1.4 Details of the Courses

• Bootcamp - refresher week

In the first three weeks of the AIV Master 1, we will try to push your knowledge in Math, physics, biology and programing to the level necessary for a fruitful and efficient year. While some of the subjects might be simple for you, other will be probably new and complicated. Luckily, you are an interdisciplinary crowd, so there should be always someone close to you that might be helpful. This is one of the most important lessons at the CRI, work together. The three weeks will take you through 5 main topics:

• Matlab programing class.• Project work and presentation of a biological subject.• Physics and Math foundation.• Biology background.• Laboratory project.

In addition to formal courses and exercises, you will have to teach yourselves by conducting a short bibliographic project in biology, a programming project in Mat-lab, and a wet-lab project in molecular biology.

• Biology annotation project

This year we will be trying something very new here, in collaboration with Melissa McCartney from Science Magazine. Yes, that Science. We would like you to help annotate several articles, in a way that has been done for articles on http://scien-ceintheclassroom.org. This is a great opportunity to go over some basic biology, help your colleagues who may be from a different field to pick up some bits that they may be missing, and participate in creating an interesting educational tool. You will work in groups, and the hope is that your work will be published on the Science website, along the annotated articles that are already there.

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• Matlab programming project

During the third week, you will work by groups of two students on a Matlab pro-gramming project. The goal of these project will be to write a (fun) game or a (useful) image analysis program. There will be different degrees of complexity for the projects to meet the different levels of the students. You will be asked to document your work on a wiki. Even if you start with no programming background at all, you can expect to have a working, fun and maybe usefull program by the end of the bootcamp!

• Lab session: Bacterial protein production via external signals

During the bootcamp, we will have a 3 afternoon sessions of basic lab work.

• Science and Medicine

Teacher: Jean-Christophe Thalabard([email protected])Hours: 7 Sessions, each for 3 hoursEvaluation: Active individual participation at each session is the basis of the finalValidation: At each session, 2 or 3 groups of 2-3 students present an article. Each student is supposed to participate to at least 2 oral presentations and being actively involved in the discussion of the presentations from the others.Deadlines: Each presenting group provides its supporting set of slides at the time of its presentation.

Overview of the class: 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 addi-tion 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. In addition research in humans raise specific issues, which are worth discussing per se. Articles will be selected in order to cover various aspects of clinical research, from early report of biotechnological and/or therapeutic advances, innova-tive designs to meta-analysis of published results when the time has come to globally evaluate previously promising approaches.

Goal of the class: This excursion into major medical journals will help the students; i) to discover their contents, their target readership and how medically- oriented articles are structured and more importantly discussed; ii) to summarize and present the results of both original and review articles in the medical field.

Requirements: no formal previous knowledge is required in this course, although an active reading of the proposed articles will take advantage of notions in biostatistics, experimental design, but also epistemology and various approaches to causality.Suggested reading: Two series of short articles published in the Br. J. Medicine by T

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Greenhalgh (http://www.tcnj.edu/~library/gorman/How-to-read-a-paper.htm) and DG Altman (http://www.medcalc.org/literature_notes.php).

• Systems Biology

Teachers: Clément Nizak ([email protected]), Gabrielle Woronoff ([email protected]), Dany Chauvin ([email protected])Hours: 12 Sessions of 2 hours lecture + 2 hours discussion.Evaluation: The evaluation is based on 2 marks, activity during discussion sessions (30%), and an exam in common with the synthetic biology and computational bio-logy courses (70%).

Overview of the class: Most of the biological functions cannot be associated to a single protein, a single gene, a single cell, or a single organism. Rather, the ability of living matter to perform amazing tasks relies on an ensemble of actors acting collectively. Those tasks, like decision making or information processing, can thus be understood only at the system level. In this course, we will first introduce basic concepts of statistical physics and engineering that have been very successful in sol-ving such problems in other disciplines. We will then show how they apply to the description of biological systems. The examples we will cover span from the molecular to the ecological scale, and will include i) self-organized subcellular systems, ii) cell functions such as regulation of protein expression, division and circadian cycles, and metabolism, iii) multicellular development regulation, iv) evolution of bio-molecules, cells, multicellulars and populations, and v) ecosystems. The course will be groun-ded on quantitative biology and modeling but will always be motivated by examples coming from biological systems.

Goals of the class:1. To become familiar with basic concepts and models of statistical physics and engi-neering: systems of many interacting (Ising) or non-interacting (perfect gas) par-ticles, modularity, robustness...2. To be able to describe biological systems that have already been studied at the system level (examples we will study during this course), as a list of units and their interactions, or as a combination of modules, and the resulting dynamics.3. Finally, to be able to describe any biological process at the system level.

Requirements: the bootcamp will be an ideal preparation to this course, there are no specific requirements otherwise. Above all, you need to be ready to look at biology with a different, highly interdisciplinary perspective, integrating most of what you will learn in other courses.

Strongly suggested readings:- From molecular to modular cell biology. Hartwell LH, Hopfield JJ, Leibler S,Murray AW. Nature. 1999- A new biology for a new century. Carl R Woese. Microbiol Mol Biol Rev. 2004- An Introduction to Systems Biology - Design Principles of Biological Circuits. Uri

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Alon 2007The course will be based on and/or inspired from many other papers that will be made available (but not required to read).

• Synthetic Biology

Teachers: Jake Wintermute ([email protected]), Ian Marcus ([email protected])Hours: 12 Sessions of 4 hours plus a final oral presentation in early January.Evaluation: The course grade will be in 3 parts. 1/3 A team presentation on a relevant paper. 1/3 Several brief written reviews of the literature and quantitative exercises. 1/3 The final project and exam.Deadlines: The final exam in early January will include a team presentation. An exactdate will be set as early as possible in the semester.

Overview of the class: Synthetic Biologists work to design and create biological sys-tems that are scientifically interesting or technologically useful. Synthetic Biology adapts concepts from the physical and information sciences, seeking to become a fully rational framework for the engineering of life. This course will introduce the major trends that drive the Synthetic Biology literature. Whenever possible, we will identify the fundamental theories and practices that unify the field and provide a foundation for future projects. Students will confront an emerging domain with an unclear definition, vague boundaries, and boundless ambition. We will wrestle with uncertainty, diffused information, conflicting intuitions and multi-disciplinarily. Course graduates will be prepared to design their own made-to-order systems, and will be familiar with the lab techniques required to bring them to life. The course includes no laboratory component. It is ideally complemented by a wet lab rotation in molecular biology or participation to the iGEM competition.

Goal of the class: Graduates from this course will be prepared to create living things of their own design, and to answer the following questions: How does a DNA sequence become working gene? How can you create complex functions with multiple genes? How can you introduce DNA to a new organism and make it work?

Requirements: Most students will be familiar with introductory-level biology or introductory-level math. In an interdisciplinary course, we expect that not many students will be totally comfortable in both subjects. Therefore we will provide access to background material as needed.

Readings:«Synthetic Biology - A Primer» by Baldwin Bayer Dickinson Elli Freemont Kitney Polizzi and Stan. Imperial College Press.«An Introduction to Systems Biology: Design Principles of Biological Circuits» by Alon. Chapman & Hall/CRC«Adventures in Synthetic Biology» by Endy, Deese, Wadey & The MIT Synthetic Biology Working Group.

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http://www.nature.com/nature/comics/syntheticbiologycomic/

• Computational Biology, Main module

«Instilling in students the feel for biological systems and for models that are used to explore them»

Teachers: Gregory Batt ([email protected]) and Dusan Misevic ([email protected])Hours: 12 sessions of 4 hours plus a final oral presentation in early January. Sessions are generally composed of lectures (2 hours) and practicals (2 hours)Evaluation: The course grade will be based on assiduity (20%), written reports on practicals (40%) and final exam (written reports and oral defense, 40%). Deadlines: Deadlines will be assigned to the two practical reports during the semes-ter and to the final exam’s report as early as possible in the semester.

Overview of the class: Using novel experimental techniques, quantitative data can be obtained on the functioning of biological systems at the molecular level. The com-plete exploitation of this novel information on system dynamics requires a model-based approach: models are proposed, analyzed and compared with respect to expe-rimental data. Using models, various assumptions on biological mechanisms can be corroborated or invalidated by the experimental data on a rational basis. Experimen-tally-validated models can then be used to make novel predictions or orient system design. The objective of this course is to introduce the model-based approach of bio-logical systems analysis from a practical point of view. The emphasis will be given on the modeling work, and on simple but important analysis methods. Such methods include state space analysis, global optimization for parameter search, and sensitivity analysis for robustness assessment.

Goals of the class:1. Testing the consistency of quantitative data produced in labs and current unders-tanding of the functioning of the observed process2. Basic understanding of modeling: how to represent reality using mathematical notions3. Basic skills of analysis: numerical simulation, robustness, parameter search4. Notions on how to model biological variability

Requirements: This course is made for people *not* familiar with biomolecular pro-cess modeling, dynamical system analysis, or Matlab programming. The sole requi-rements are therefore elementary calculus and notions of molecular and cellular bio-logy, as well as a strong motivation to learn.

Recommended readings:- Systems Biology in Practice: Concepts, Implementation and Application, by E Klipp, R Herwig, A Kowald and C Wierling, Wiley, 2005- Modeling and simulation of genetic regulatory systems: a literature review, by H. de Jong, Journal of computational biology, 2002

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• Computational Biology: Rule based Modelling

Teachers: Vincent Danos ([email protected]), Jérôme Feret ([email protected]), Jean Krivine ([email protected])Hours: 4 Sessions of 4 hours each (2 hours of lectures, 2 hours of practical works)Evaluation: There will be a short project after the class due for after the Christmas holidays.Deadlines: to be announced

Overview of the class: In this class, you will learn a new way, called rule-based model-ling, to perform mechanistic modelling which is very different from that of the more usual approach through ODEs. This approach builds models by writing,in a simple formal language called Kappa, rules that describe directly the possible interactions between proteins; these models can be equipped with rate laws and then simulated and analyzed with open source software tools (that we will provide).The class is pri-marily practical where you will develop, think about and analyze a series of increasin-gly complicated systems using Kappa. There is also some pure lecturing time in order to explain the novel analysis tools offered by Kappa.

Goal of the class: The main aim of the class is to help you to develop your intuitions about how signalling networks operate. The use of rule-based modelling makes it easy to try out variants of a model, which sometimes have very different behaviour,and so there is a strongly emphasis on exploratory learning. You will also learn some specific technical material, notably about stochastic simulation, that complements what you have learned about ODE-based deterministic simulation in other classes.

Requirements: There are no absolute prerequisites for this class although a passing familiarity with programming might ease the initial learning curve of writing rules and executing models and some basic intuitions about probability theory will helpfor understanding how simulation works.

Reading:- D Bray, S Lay. Computer-based analysis of the binding steps in protein complexformation. PNAS 1997.- A Goldbeter, D Koshland. An amplified sensiti-vity arising from covalent modificationin biological systems. PNAS 1981.- L Segel. On the validity of the steady state assumption of enzyme kinetics. BMB1988.- C-Y Huang, J Ferrell. Ultrasensitivity in the mitogen-activity protein kinase. PNAS1996.

• Statistics

Teachers: Eugenio Cinquemani, Valentina Peschetola (TD)Hours: 10 sessions of 4 hours each (2 hours teaching and 2 hours practice per session)Evaluation: The final grade will be determined on the basis of activities developed in the course and also on a final exam. Evaluation will assess the assimilation of statisti-

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cal concepts as well as technical skills.Deadlines: to be announced

Overview of the class: We will address the subject from the perspective of inference. In the beginning of the course, we will overview and discuss descriptive statistics and poll-based experiments to motivate the need for a probabilistic modelling framework and develop a feeling for statistical reasoning. Then, we will discuss commonly used methods of estimation and hypothesis testing (e.g. comparison of means, linear re-gression, analysis of variance), based on rigorous but simple mathematical develop-ments and emphasis on conceptual issues, and work on their application to example problems in the practical sessions.

Goal of the class: First aim is to develop the students’ critical thinking for the connec-tion between statistical reasoning and real-world problems. Second aim is enabling students to determine appropriate methods for the analysis of different datasets, star-ting from a toolkit of common inference techniques.Requirements: Calculus (including integration)

• Dynamics of Living Systems

Teachers: Emmanuel Farge ([email protected]), Timo Betz ([email protected]), Hours: 9 Sessions of 4 hours each + oral presentation of each group. You will form groups of 2-3 students, each group is working on a separate project.Evaluation: The evaluation is based on 3 marks, Implication in the class, a written report on the project and an oral presentation.Deadlines: There is a fixed deadline for the written report which is the first Monday in the new year. You need to turn in the report via e-mail to the teachers.

Overview of the class: While you will learn in many other classes the theoretical foun-dations of complex systems, you will be able to apply these newly acquired knowledge in this class. The main idea is to provide you with a set of previously published papers, each describing a dynamical process that happens in living systems such as develo-ping organisms, tissues or the single cell level. Each of these papers combines expe-rimental knowledge with a mathematical model to understand the complex situation it describes. To reproduce the experimental data, the mathematical models are closely investigated in a computer simulation, and one goal of the class is to reproduce these simulations with your own code. In the second part of the class we will try together with you to further develop the project in an individual way you choose.

Goal of the class: Understanding a complex mathematical model of a biological pro-cess by analyzing the original paper. Reproducing the results using basic simula-tion methods Critical analysis of the reproduced model and the development of a constructive criticism. Develop your individual way to improve previously published work.

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Requirements: To take maximal advantage of the class you should have a general idea of programming, ideally in the Matlab environment. You will furthermore need to have a good understanding of calculus, and of the fundamental physical principles involved in signaling and motility. This includes rate equations, diffusion and force generation. Besides this you will need a very good background in cell biology and signaling, and fundamental knowledge of development and biochemistry.

Reading:- J. Lewis, Autoinhibition with transcriptional delay: a simple mechanism for theze-brafish somitogenesis oscillator.- Eldar et al, Robustness of the BMP morphogen gradient in Drosophila- Sprinzak et al, Cis-interactions between Notch and Delta- Gardner et al, Construction of a genetic toggle switch in Escherichia coli- Mein-hard et al, Pattern formation in Escherichia coli

• Introduction to quantitative biology: course Teachers: Nicolas Minc ([email protected] ) , Guillaume Ro-met-Lemonne ([email protected])Hours: 4 Sessions of 4 hours each. Each session will alternate between 1h of lecture and 1h of practical exercise made by groups of 2-3 studentsEvaluation: The evaluation is based on 2 marks: Implication in the class and a short MCQ. The mark will be integrated with the experiment sessions (see below). Overview of the class: The general aim of the course is to introduce students to the cross-talk between physical and biological mechanisms in the regulation of basic bio-logical processes. The course will particularly focus on the cytoskeleton and its impact on cell growth, polarity, morphogenesis and division. Half of the course will be dedi-cated to introduce basics of microtubules and actin regulation and the other half will focus on discussing examples that underlie their role in different cellular contexts. This course will serve to introduce basic principles and an outlook of modern tools in biophysics as an introduction to the real experimental course. Key question that will be addressed include: how do cytoskeletal elements generate forces? How are these forces integrated by cells to position organelles or generate cellular-scale forces? How are these processes regulated in different organisms, at different scales? Goal of the class: The course will provide students with a good knowledge of cytos-keleton regulation, and general biophysics. A number of classical experiments and techniques will be discussed. It will highlight differences between cell types, biologi-cal scales and conserved design principles or rules. Students will learn to observe, ask questions, formulate hypothesis and propose simple tests/experiments. Specific goals:1. Actin and tubulin versatility : different ways to differentiate subunits (free mono-mers, in filaments, at ends, + nucleotide state)2. Why are actin filaments and microtubules polarized.

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3. What makes MTs stiffer than actin filaments.4. How cytoskeletal filaments are organized the way they are in cells.5. Basics of molecular motors (what parameters characterize them).6. Cytoskeleton force generation and division positioning7. Orders of magnitude and scaling concepts of cytoskeleton mechanics in cells8. Mechanisms and mechanics of cytokinesis9. Cytoskeleton and cell shape determination Requirements: To take maximal advantage of the class you should have a broad idea of how cells function (What is a gene, a protein, the plasma membrane…), and a basic knowledge of physics principles (What is a force, a torque, an energy...). Reading: Grill, Science. 2003 Jul 25;301(5632):518-21.Dogetrom et al, Curr Opin Cell Biology 2005Kirschner M, Mitchison T. Cell. 1986 May 9;45(3):329-42.Minc, Trends Cell Biol. 2012 Apr;22(4):193-200.Pollard, TD Science. 2009 Nov 27;326(5957):1208-12.

• Introduction to quantitative biology: experiments

Teachers: Matthieu Piel ([email protected]), Anne Paoletti ([email protected])Hours: 6 days of 8 hours each. You will form groups of 2-3 students, each group is working on an individual project.Marks: The evaluation is based on 3 marks: implication in the class, a written report on the project and an MCQ.Deadlines: There is a fixed deadline for the written report which is the first Monday in the new year. You need to turn in the report via e-mail to the teachers. The MCQ will take place one week after the last day of the class and it will be testing your understanding of the methods you have used in your project, so ask questions on how things work and listen to the answer!

Overview of the class: During this class you will design, execute and interpret experi-ments. There will be several types of experiments proposed, all sharing one characte-ristic: there is a quantification based on imaging, then data analysis. You will use the fission yeast S. Pombe as a model organism and design quantitative experiments to understand how it grows and achieves its particular rod-like shape.

Goal of the class: The general goal is to learn how to answer a question by yourself, through an experimental approach. The question has to well formulated, the experi-ments well adapted to answer it and the result well interpreted (with its limitations). By letting you, as much as possible, design the experiments, run them and interpret them, we hope that you will get ready for the long learning path of experimental sciences. You will be presented the model system and the available tools. Then you will spend an afternoon designing experiments in details, with the goal to come up

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with a schedule for the next days of experiments and precise protocols. There will then be four full days performing experiments, acquiring data on microscopes and quantifying them by image analysis using the ImageJ software. During these days, you will learn not only how to perform these particular experiments, but also how to check the quality of the data, and to decide whether more experiments need to be done, from a first set of analysis. Extracted data will then be further analysed and interpreted, going back and forth between experiments and analysis until there are enough data to reach a conclusion. Each group will shortly present its results and dis-cuss them in the last session. The goal of this last part is to judge whether the whole process led to an interesting answer or not, and to discuss about the next steps to take to go further if you were starting a longer term set of experiments.

Requirements: During the course you will learn all the required experimental tech-niques, but you need to have some background knowledge on the biology and the physics involved. This will be provided during the course organized by Nicolas Minc and Guillaume Romet-Lemonne, which will take place before this course.

Reading:- A journey into space. Hayles J, Nurse P. Nat Rev Mol Cell Biol. 2001 Sep;2(9):647-56.- Microtubule-dependent cell morphogenesis in the fission yeast. Martin SG. Trends in Cell Biol. 2009 Sep;19(9):447-54.- Osmotic stress signaling and osmoadaptation in yeasts. Hohmann S. Microbiol MolBiol Rev. 2002 Jun;66(2):300-72.- Mechanical forces of fission yeast growth. Minc N, Boudaoud A, Chang F.Curr Biol. 2009 Jul 14;19(13):1096-101.- Physical mechanisms redirecting cell polarity and cell shape in fission yeast.Teren-naCR, Makushok T, Velve-Casquillas G, Baigl D, Chen Y, Bornens M, Paoletti A, PielM, Tran PT. Curr Biol. 2008 Nov 25;18(22):1748-53.1.5.

• Scientific communication

Teachers: Matteo Merzagora, TRACES-ESPGG (with contributions from Anissa Benchelah, Richard-Emmanuel Eastes, and other members of the groupe Traces)Hours: 9 sessionsMarks: The evaluation is based on three criteria: the participation to the class dis-cussions and flash-workshops; the delivery of a 10 minutes presentation with visual supports on the subject of the student internship; the realisation of a group project of public science communication.Deadlines: The scientific presentation is due at mid term (after 4 sessions); the group project is due at the one-before last class.

Overview of the class: The course focuses on the relevance of communication in the various aspects of the scientific activity. It presents an overview of the communica-tion skills necessary within the scientific community, as well as when addressing the general public. In fact, there are a great variety of activities in the life of a scientists in

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which communication skills play a major role: writing papers, reading papers, giving seminars, discussing with colleagues, communicating within a lab or a working group, explaining your job to your family, writing grants, teaching, giving public lectures, talking to journalists, … Communication is more a set of skills than an organised body of knowledge. Therefore, the course focus on helping the students to learn how to learn from the observation of communication products they encounter in their life (posters, oral presentations, scientific papers, popular press, meetings at the cafeteria, movies, family conversations,…).

The main topics treated are:1.What is science communication? Who communicates science? To whom? And why?2. Using your voice and your body: inputs from theater techniques (led by a profes-sional actress and trainer)3. The oral presentation and slides preparation: structure, tips and tricks4. Writing for scientists or for the general public: main differences and case studies.5. Science in society and public perception of science6. Science in the media, science and cinema, science museums, citizen science and public participation, … (one topic, depending on where the discussions will lead us)Besides this series of lectures, each session will includes practical exercises, specifically focusing on peer-learning activities. In addition, the students are expected to prepare one ten-minutes presentation on the topic of their internship, and one science com-munication projects developed in binomes.

Goals:• Acquiring awareness of the role of communication in the daily work of a scien-

tists• Acquiring awareness of the importance of science in society and society in

science• Acquiring observation skills, i.e., learning to observe other scientists’ communi-

cation to copy the pluses and avoid reproducing the minuses.• Acquiring a series of practical skills for preparing and delivering an oral pres-

entation, including the use of the voice and body, the capacity to interpret the audience’s needs and expectations and reacting accordingly.

• Acquiring a taste for quality in communication.

Reading:For a quick and simple introduction: • Frank Burnet, Why and how to communicate your research (http://frankburnet.

com/why-and-how-to-communicate-your-research-2/• Frank Burnet, Taking science to people (http://frankburnet.com/free-down-

load-of-taking-science-to-people-2/) Books for more in-depth work:• David Bennet, Richard Jennings (Eds), Successful Science Communication:

Telling It Like It Is, Cambridge University Press, 2011• Richard Holliman, Jeff Thomas, Sam Smidt, Eileen Scanlon, Elizabeth White-

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legg (Eds), Practising Science Communication in the Information Age: Theori-sing Professional Practices, The Open University, 2009

• Internship / iGEM

Please refer to the «Internship section» at the end of this booklet to get tips on how to find an internship.

• What we expect from you?1 - Contact labs, visit labs, find your internship. Start this as early as possible. 2 - Early november, we’ll invite you to communicate your potential internship through a web form. We will than come back to you mid november to let you know if we accept your proposition. This step is mandatory.3 - You will than have to start to sign the «convention de stage» as soon as possible (mid-December at the latest). Not that it may take some time to sign this convention, and you need it to start the internship. 4 - Start your internship on the 1st of February.

• Internship EvaluationAt the end of the internship you will have to give an oral defence and you will have to turn in a short report containing: the project title and the name of your supervi-sor and its affiliation; an abstract (200-300) words detailing background, objective, methodologies, results and perspectives of the internships; one scheme describing your research subject and a figure or graph describing your main results together with a figure caption. Usually the oral defence takes place in the first week of July, and you will have to turn in the report the Monday of the defence week. Note that attendance to the presentation of all students is mandatory.

1.5 Who to Contact ?• • Administrative questions: Laurence Dominguez, the AIV Master secretary, she

will be able to guide you or put you in contact with the right person to help you out

• Academic enquiries concerning the M1: Timo Betz.• General enquiries about the AIV Master: Ariel Lindner or Pascal Hersen. Please

send us an email to make an appointment. We will usually be available at the CRI on Friday afternoons.

Please ask your other questions directly to your teachers.

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1.6 What’s next ?At the end of the Master 1, and given that you have passed all exams we will discuss with you the opporunity for you to continue with us in M2. Usually all students that want to stay with us, can do so. However, if for some reason you prefer to switch to another Master program that is more specialized and focus on your favorite research topic, we’ll help you to make the transition.

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2. M2/AIV

2.1 Content & Planning of the year

The year starts by a one week workshop at Sèvres and then students are expected to perform 3 internships of three months each, while preparing and attending the courses on Fridays.

Here are the main important dates for the M2.

Workshop at Sevres 07/09 - 12/09Internship I : 15/09 - 31/12.CRI Opening Days : 01-02/10Internship I defense : 17-18-19 december Internship II : 07/01 - 05/04Internship II defence : first week of april (joint event with FdV)Internship III : 15/04 - 15/07Reharsal of FdV application : end of may (TBA)Internship III defence : early July

2.2 Details of the course

• Workshop at Sevres (CIRP)

The workshop, set in Sèvres (near Paris), intends to assemble free spirited students and researchers from broad scientific backgrounds to conceive creative projects at the interface with Life Sciences. This year will combine newcomer students of the FdV PhD program, 2nd year AIV master program and will host students of the 1st year AIV master program and the 1st and 2nd years of the Licence FdV program on Friday. The CIRP workshop attempts to provide the primary basis for collegiality and communication through dialogue and brainstorming on open questions in Life Sciences.

• Aims of the 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

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» To learn how to write a research proposal. » To discuss scientific questions thoroughly. » To learn to interact with people from different backgrounds.

• CARA - Critical Analysis of Research Article

Format : 2 hours/week. All Fridays at 15:00Remarks : MandatoryValidation : Mark>10; 80% of active presence in seminars and comments contribu-tion in the workplace

Course objective:Develop the student’s ability to read and critically interpret papers from high quality journals. Through this exercise the students will be exposed to a large spectra of inter-disciplinary research domains and methodologies.

Develop the student’s ability to prepare and present a scientific talk (in English). Emphasis will be given to the talk’s structure, slides, interaction with the public and scientific language.

This course is built of a series of seminars, each prepared by two students from dif-ferent backgrounds, presenting in detail an interdisciplinary 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. All students are expected to participate in the course forum, contribu-ting their insight and questions on the article at hand.

The course is supported on the moodle platform by:

A general forum for practical information

The main ‘Workplace’ where each ‘entry’ corresponds to a given seminar. It is here that every pair presenters should put their abstracts and receive comments from ALL the course session participants. Note that we will have two sessions in parallel and that you have to make your participation choice for all the sessions by Thursdays. When a session is full, you’ll have to attend the other one.

The ‘CARA database’ where all supporting files and articles should be placed.

The ‘presentations’ where your final presentation file (ppt or pdf ) should be placed.

Deadlines & Organization1. At least 8 days before each presentation, place your article in the ‘Workplace’ with your own abstract placed in the forum; include hyperlink(s) to your entries to the database (including any Supporting Material).

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2. All students participating in the session have to add their comments at the Work-place entry (follow instructions therein) no later than 3 days before the presentation (e.g. Tuesday).3. A Short debriefing of the presenters by the AIV mentors will take place after the seminar focusing on the science discussed as well as on the quality of presentation. To this end, some of the sessions may be filmed.4. At the end of the two parallel sessions we will group everyone together. Each sub-group will debrief their colleagues (5-10 minutes) about the session they did not attend.5. Post your presentation file (ppt or pdf ), taking into account the post-presentation comments in The CARA presentations database (deadline: Monday. Write down the summary of comments received as post-evaluation.

• BibSyn - Bibliography Synthesis

Format : 2 hours / week, Fridays at 15:00Remarks : MandatoryValidation: Mark>10; 80% of active presence in seminar and Comments contribution in the Workplace

The course consists of a series of seminars, each initiated by two students from dif-ferent backgrounds, presenting their review of scientific literature concerning a sub-ject of their choice.

All students of the course are expected to contribute for each session their point of view on the subject of choice by:

1.reading (at least one) peer-reviewed paper or well-documented website.2. posting it in the database together with writing a 200 word paragraph describing the resource and its relevance to the review subject. This should be done no later than two days before the presentation.

Organization1. post the Title and initial abstract of the review. Regardless of your presentation dates, start a discussion topic with your Review Title in the Forum and enter a preliminary summary of what you have in mind to work on. This summary (300 words) should be finalized 2 weeks before your presentation.

2. Upload your selection of 10 top articles to the course database. (at least 2 weeks before the presentation)

3. Present a concise review, treating their chosen subject from different perspectives - their own as well as those raised in the forum. (1 hour including discussion). The slides file (pdf/ppt) should be sent to the tutors/teachers a week before the presenta-tion in order to receive their feedback!

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4. Include a discussion of one emerging open question arising from their review and present detailed experimental/modeling approaches attempting to resolve it. (30 min. including discussion)

5. Post your final presentation file at the day of your presentation.

• ZOIO - Zoom In - Out

Format : 2 hours/week. All Fridays at 15:00Remarks : MandatoryValidation: Mark>10; 80% of active presence in seminar and contribution in the workplace

Rules of the game:This series of seminars is based on a scientific book. It split into two parts: i) wri-ting, presenting and reviewing an interdisciplinary research project that may be inspired by the book and (ii) a book review.The choice of the book is crucial. You should start to find it early in the year. The teacher will validate the choice and orient the students if necessary. I. Research project: (i) The applicants write a detailed interdisciplinary project with theoretical/mode-ling and experimental approaches in the form of a 3-year grant application, using the form attached (‘Project Proposal’). Teachers will mentor the groups during this preparation of the project (3 Friday afternoon sessions). ALL projects should be submitted at the same time (end of March).Guidelines: The project should be realistic and based on the literature. Questions should be ambitious, risky, innovative and feasible. The preliminary data that are crucial for the project could be “imagined”. The titles and subtitles (text in red) should be kept and the text in blue should be removed. The work should be equal-ly divided between the members of the group. (ii) The reviewers grade the project individually and anonymously according to provided evaluation criteria and send the scores to the teachers before the indica-ted deadline. The review panels are composed of members from different groups. One will know to which panel he/she belongs only when he/she receives a grant to review. On the review date, the panels meet, chose a president whose role is to moderate discussion, make the final score and write 2-3 pages review commen-ting on 3 evaluation criteria and the budget. Students who are not in Paris, should send their individual reports that will be taken in consideration. The same day, reviews are sent to the teachers and applicants. Teachers will be present during the panel meetings as observers.(iii) The applicants take into account the review they received and present their research project (20 min presentation and 30 minutes questions).Guidelines: If you agree with reviewers comments - change your project accordin-

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gly. If you do not agree - prepare to defend your point of view. (iv) An editorial board will be formed by teachers. They will judge whether the review process was constructive and fair. (v) Final evaluation. After all projects are presented, all reviewers will discuss to-gether all projects, taking into account the written project, scores given by the panels and quality of the oral presentation. Final score and «post-presentation» evaluation will be given after discussion. II. Book review:Using a scientific book as a starting point, group of students present the main the-sis of the book. This will be complemented by their own critical review of the book and presentation of the open questions the book has raised. A list of potential books (all available at the CRI library) is attached below. Total time for presentation is 1h.Guidelines: Presentation could be a theater play, a song, a film, a painting, an ex-periment, a debate, anything…. Express yourselves and be creative!

• Internships

You will have to do three internships. You can consult the «internship» section at the end of this booklet to have some tips of how to find an internship. Note that there are several rules that apply :

1 - The first internship must be done near Paris. More precisely, we want you to attend all the courses ans events of the first semester. You can go away from Paris, but you need to be back in Paris for the courses every week.2 - The Second or Third internship can be done abroad. The duration of an internship abroad is also of 3 months. The third internship can be, however, prolonged during the summer. In case you go abroad, you must make sure that you will be there for the internship defense (early April, early July).4 - We will ask you to participate to the moodle and to be back for your presentation if possible. We will also ask you to attend seminars, courses or a MOOC to compen-sate for your absence.5 - Exceptions to these rules might be possible depending on your particular situa-tions. As usual, come to us to discuss your projects. The earlier, the better.

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2.3 Who to contact ?

For general enquiry about the master, please do contact the secretary during the opening hours of the secretariat. If you want to meet with us, ask us an appoint-ment. We’ll be able to meet with you on friday before or after the session. For an urgent matter, contact us directly by email.

For specific request regarding one course, please do ask directly to the person in charge :

Sevres : Stéphane DouadyCARA : Anna Maria LenonBibSyn : Danijela VignjevicZOIO : Olivia du RoureInternships : Pascal Hersen.

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FOSTER

Formation pour l’Ouverture des Sciences, des Technologies, de l’Education et de la Recherche

Fostering Open Science, Technology, Education and Research

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3. FOSTER/M1

3.1 General InformationThe first year of the Master is designed to teach the basics of a the future actors of education. Philosophy of learning, technologies for education but also cognitive science and learning by doing, you will be trained in all the matters that form the core of an innovative education through research. Be involved, share your knowledge and expertise and you will spend a very fruitful year. We expect you to invest a lot of your skills and energy in the different courses. This means to prepare all courses, in particular by reading articles and books, to ask questions when you don’t understand something and to be proactive in classes.

You will have to register on the Moodle and the Google Apps platform. These are very powerful tools and you’ll have to use it for practically every course. Teaching materials (articles, PDFs) will be posted by the teachers for you to read and think on before the courses. You will also have to exchange using the dedicated forums. It’s therefore important for you to be at ease with this tool as soon as possible. Note that you’ll also be evaluated on how much you participated. The spirit of the Master is to responsibilize the students and to maximize exchanges amongst them. As a result it is crucial that you attend all courses. Students are also expected to be on time and to respect deadlines. If you cannot come to a course, let the teachers know about it beforehand. Similarly, if you feel that you are not going to be able to meet a deadline, or if you have a problem with a course, do let us know as soon as possible. It’s much easier to find a solution if we are aware of the problem.

3.2 The content of the first year (M1)

• First Semester (September - January)

The first semester starts by a 3 weeks long bootcamp that gives you the start to the year in IT particularly. Since you all come from different backgrounds we try to give you common knowledge on coding that you will have to use to design your tools and feed your experimentations. You will also have several conferences to discover the world you will be entering : education, technology, social entrepreneurship.

After this bootcamp, several core courses will take place every week. You will learn the theoretical and practical concepts that are required to act for opening education technology, science and research..

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UE1 --- Serious Games (A. Taly)UE2 --- Learning by doing (J. Chevrier)UE3 --- Science Communication (JM. Galan)UE4 --- Philosophy of learning (A. Janvier, S. Audidière)UE5 --- Technologies for learning (S. Pène)UE6 --- Pedagogical Innovation (S. Pène)UE7 --- Open Science (S. Mesmoudi, K.Bazin)

You need to validate 5 courses, meaning to have a final grade equal or larger than 10/20. Grades will be based on your attendance, oral participation in classes, quality of your homework and success to the final exam. Although you need to validate 5 courses over the 7 that are proposed, we do expect you to follow all courses and pass all exams. For your final grades, we will keep the 5 best ones. Regarding the grades, please do note that, by definition their meaning is very limited - what does that really mean to have 14/20 to an exam? How much does that tell about your skills and deep understanding of a scientific domain? This is why we will also provide you with a written evaluation, detailing what are your strong skills and in which aspects you should improve for each courses. We will also provide you with mid-term oral eva-luation through an informal and interactive discussion between the master organizers and the M1 student.

• Second Semester (February - July)

The second semester will focus on practical work. You will spend at least 5 months in a research lab or in a company. You will also have some mandatory events at the CRI :

UE2.1 --- Seminars UE2.2 --- Cognitive Science (E. Pasquinelli)

Both classes will be evaluated based on your attendance, oral participation and pre-sentation.

• Research Internship (February - June)

The research internship is an integral part of your training. The internship will be full time, and should ideally consist in a defined project that will lead to results within the 5 month period. Ideally the internship runs from the beginning of February to the end of June, but this can be subject to individual changes as long as the intern-ship llasts at least 5 month. Any internship projects related to education through research research are possible. You will have to turn in a short report containing: the project title and the name of your supervisor and its affiliation; an abstract (200-300) words detailing background, objective, methodologies, results and perspectives of the internships; pictures, schemes or any visual representation of your activity are wel-come. Usually the oral defence is in the first week of July, and you will have to turn in the report the Monday of the defence week. Note that attendance to the presentation

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of all students is mandatory. See the internship section at the end of this booklet for more details and advice on how to find an internship.

• IGam4ER competition.

As an alternative to this long internship, you can create an IGam4ER team. Every year the CRI organize a serious games competition in Paris and one of your courses will deal with it. If you are interested in the matter you could build a team for the CRI and prepare your project for the competition. Since it is held in December you will have to organize yourself to stay in the steam up to that date. For those continuing with us in the second year of the master, this means that your first internship of M2 will be dedicated to finishing the IGam4ER project.

3.3 Planning of the Year (2014-2015)The complete agenda can be found on the Master web page. Note that some dates may change during the year, so do not hesitate to ask us if you have a doubt. Here are a few important dates to remember:

• Bootcamp - starting on the 11th of September.• Discovery days - 1st and 2nd of October • Deadline for internship «convention de stage» - 28 of November.• iGam4ER: 13-14th of December• First semester exams - January 19th to 24th .

3.4 Details of the Courses

• Starting the year / Refresher weeks

In the first three weeks of the FOSTER Master 1, we will try to introduce you to our ecosystem. While some of the subjects might be easy for you, others will be probably new and complicated. Luckily you are an interdisciplinary crowd, so there should be always someone close to you that might be helpful. This is one of the most important lessons at the CRI, work together. The three weeks will take you through:

-Arduino at the Open Lab-Python coding language-FOSTER’s Ecosystem-Opening days.

• Arduino at the open lab / 15th-19th of September / Kevin LhosteDiscover the possibility that open technology gives. Arduino is an open hardware, it is one of the wonderful tool you can use to change your environment. Easy of access it is the perfect entry to the robots science. The Open Lab is one of the major project of the CRI, it gives access to technologies

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and tools that can help you to test and build your ideas throughout the year.

• Computer programmation : Python / 22nd-26th of SeptemberComputer programmation is one of the basics everyone should learn. It is everywhere in our world and you cannot decently leave it to a small group of high trained compu-ter programmer. What is more coding is a way to better understand what is education in the XXIst century: you will learn by trying and testing, you have the right to make mistake and there is more than one answer but in the end you will be able to really create something. Each day you will have to face new challenges progressing in dif-ficulties one after the other. During this intensive week, you will have no obligation of results but we ask you to go as far as you can each day, to face the problem and try to solve it.

• FOSTER’S Ecosystem / 19th - 30th of SeptemberEducation is no longer the matter of an institution. The sharing of knowledge is a central question for many among the society and school is not by far the only place where you can find them. You are interested in building the future of education you have to meet with these who change it now. • Léa Peersman-Pujol• Grégoire Serikoff • Ange Ansour

• Preparing the Opening daysIn order to prepare your presentation for the opening days, Viviana Gozzi will help you through the process of designing your ideas.

• Serious Games

Teachers : Antoine TalyHours : To be determinedEvaluation : Every part is evaluated : fundamental courses (15%), report on a peda-gogical sequence (20%), presentation (15%), game (50%).Deadline : To be determined.

Goal of the class : To discover the serious games and their use in teaching. Several games will thus be studied and an analysis will be asked. At the end the students will create an original game. A secondary goal is to introduce the students to flipped classrooms. Students will have to prepare the courses with several documents pre-viously given to them. The course is then mainly active.

• Learning by doing

Teachers : Joël Chevrier, Léa Peersman-PujolEvaluation : Project PresentationHours : 3x6h in the lab, 2x3h to analyse the results, 26h to build your own project.Deadline : To be determined

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Goal of the class : The best way to understand the meaning of what you learn and to be able to create is to do it by yourself. In the Openlab students will discover scientific principles through their own senses. With that spirit of experiment in mind they will be asked to design a project fitted to their own ambition.

• Science Communication

Teachers : JM Galan, Simon Houriez, Cathy Dubois and Michel AvignonHours : 20h of science communication lectures, 5h of case studies, 18h of science communcation towards death public.Evaluation : To be determinedDeadline : To be determined

Goal of the class : To understand what is science communication in a time of tech-nologies. To discover the wide spectrum of mediation (from museum to classroom, from newspapers to twitter). To enhance your capability to express specific knowledge to specific public.

• Philosophy of learning

Teachers : Antoine Janvier, Sophie Audidière, Robin Holmes, Stéfanie MassonHours : 12h lectures, 9h reading, 19h workshopEvaluation : To be determinedDeadline : To be determined

Goal of the class : The aim is to understand the philosophical basis of a XXIst century education. Through readings, lectures and workshops students will reflect on their ambition and projects for education.

• Technologies for learning

Teachers : Sophie Pène, Jean-François BonnetHours : 10h of lectures, 40h of digital project buildingEvaluation : To be determinedDeadline : To be determined

Goal of the class : The students have to conduct together an whole digital project, including user experience design, technology, strategy, publishing. The result is a per-sonal portfolio and a cooperative learning MOOC.

• Pedagogical Innovation

Teachers : Sophie Pène, Elie SloïmHours : 50h Evaluation : To be determinedDeadline : To be determined

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Goal of the class : Why « Innovation » is now matched with « education » ? Students will conduct an historical approach, a critical analysis and a context-based research. We hope enlighten the use and the meaning of « Innovation » (concept, management project, public policy…). Our aim is to describe the global EdTech (Education Tech-nology Services) and its expansion toward global digital economy, social innovation, change making, the sharing economy ) with a focus on the MOOC and the new issue of data driven improvement.

• Open Science

Teachers : Salma Mesmoudi, Kilian Bazin, Cathy Dubois and Michel AvignonHours : 43hEvaluation : To be determinedDeadline : To be determined

Goal of the class : To discover scientific studies based on open source, analysis and treatment of data. To discover the field of datadesign. To use the different tools at hand to represent data and the communication strategy coming along with. to per-ceive the link between scientific data and societal challenge (through the example of Haiti). To deal with citizen science, citizen mapping, benchmarking.

• Cognitive Science

Teachers : Elena PasquinelliHours : 11 sessions- 32hEvaluation : To be determinedDeadline : To be determined

Goal of the class : To be able of propery using data produced by cognitive science. To be able to collaborate with cognitive scientist to improve the learning process. To know what cognitive science can help you with and what it cannot do. To be familiar with the specific ethical and methodological issues of coginitve science.

3.5 Who to contact?• Administrative questions: Julie Camonin, the IIFR secretary. She will be able

to guide you or put you in contact with the right person to help you out.• Academic enquiry : Sophie Pène• General enquiry about the Master AIV: Sophie Pène or Pascal Hersen. Please

send us an email to make an appointment.

Please ask your other questions directly to your teachers.

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4. FOSTER/M2

4.1 Content & Planning of the yearThe organization of the year is rather simple: it starts by a one week workshop at Sèvres and then students are expected to perform 3 internships of three months each while preparing and attending the courses on Wednesdays.

Here are the main important dates for the M2 FOSTER.

CRI Discovery Days : 1st -2nd October (mandatory)IGam4ER competition: 13-14 of DecemberInternship I defense : 17 of december.Internship II : 12/01 - 03/04Internship II defence : first week of April, TBA (joint event with FdV and AIV)Internship III : 13/04 - 03/07Internship III defence : early July

4.2 Details of the course

• Workshop at Sevres (CIRP) - Joint event with AIV / FdV

The workshop, set in Sèvres (near Paris), intends to assemble free spirited students and researchers from broad scientific backgrounds to conceive creative projects at the interface with Life Sciences. This year will combine newcomer students of the FdV PhD program, 2nd year AIV Master program, 2nd year FOSTER Master program and will host students of the 1st year AIV and FOSTER Master program on Friday. The CIRP workshop attempts to provide the primary basis for collegiality and com-munication through dialogue and brainstorming on open scientific questions.

• Aims of the 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» To think and express your ideas more clearly.» 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.

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• Review on Pedagogical Innovation (REPI)validation: group work, reading, report, presentation

The aim of the workshop is to build critical and creative tools, to define a methodolo-gical and scientific field around the FOSTER master through the review of the data on education and technology.

• Analysing Pedagogical Innovation (API)validation: group work, reading, report, presentation

Any pedagogical innovation is not bound to be worth the pain, the aim of the works-hop is to understand the critical factors that can make it a success after you have determined it is useful to your goals. Analysing data and previous experience you will make these factors appears.

• Design, Creation and Evaluation of an Innovative Project (DECEIP)validation: group work, reading, report, presentation

Hopefully with our help and your internships experience, you will determined a pro-ject you would like to see happen at the end or after your master. This workshop will help you design it deeply and build it.

• InternshipsYou will have to do three internships. You can consult the «internship» section at the end of this booklet to have some tips of how to find an internship. Note that there are several rules that apply : 1 - The first internship must be done near Paris. More precisely, we want you to attend all the courses ans events of the first semester. You can go away from Paris, but you need to be back in Paris for the courses every week.2 - The Second or Third internship can be done abroad. The duration of an internship abroad is also of 3 months. The third internship can be, however, prolonged during the summer. In case you go abroad, you must make sure that you will be there for the internship defense (early April, early July).4 - We will ask you to participate to the moodle and to be back for your presentation if possible. We will also ask you to attend seminars, courses or a MOOC to compen-sate for your absence.5 - Exceptions to these rules might be possible depending on your particular situa-tions. As usual, come to us to discuss your projects. The earlier, the better.

4.3 Who to contact ?For general enquiry about the Master, please do contact the secretary,Julie Camonin, during the opening hours of the secretariat or by email: [email protected]. If you want to meet with us, ask us an appointment. We’ll be able to meet with you on Wednesdays before or after the session. For specific request regarding one course, please do ask directly to your teacher.

INTERNSHIPS

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5. INTERNSHIPS

Finding a lab that fits your research interest usually takes some time, both to respect the administrative deadlines and to make sure that you will fit nicely in your hosting research team. Here are some tips and indications.

• Internship Process in the master AIRE

We ask you to find yourseld your internships. They can be done in a laboratory, an association, a company, a NGO, etc... The pedagogical team will validate your propo-sition before you can start your internship. This is how it works :

1 - We will send you an email with a link to a web app. You will have to fill this form, (before the deadline!). Note that you will have the possibility to comeback to this form to update your choice. Whatever your situation, you must fill this form, this is our only way to track your progress and to help you! 2 - When filling the form, take the time to do it the right way. We are using this both to validate your choice and to record the activity of our students. This means that the adress, phone, contact, names of your labs must be accurate. We also need a title and a real abstract that explains in a few lines what you will do during this internship.3 - The Pedagogical team will quickly assess your proposition and, usually, we will send you an email saying that your internship has been validated. This will usually be done one month before the start of your internship.4 - You will then have to fill the «internship agreement» (convention de stage) that you can find on the website of your university (Paris Descartes or Paris Diderot). As explained below, this can take some time so do this as soon as you received our green light.5 - Start the internship, work hard and have fun.6 - Prepare an oral presentation for your internship defense.

For the M2 students, this process occurs several time during the year, meaning that you will have to find your second internship while doing the first one, and find the third internship while doing the second one. As usual, if you have questions, if you are facing a difficult choice, or require to adapt the framework of internship, ask us as early as possible.

For the FOSTER students : You will have to turn in a short report on your web page and to the jury containing: the project title and the name of your supervisor and its af-filiation; an abstract (200-300) words detailing background, objective,methodologies, results and perspectives of the internships, visual representation of at least some part of your activity or results, representation of your institution work environment. It will also be the time to present the portfolio you will have to build during the year gathering online your experimentation, observation and wondering.

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• How to find an internship ?

You may ask how to find an internship. It’s actually an interesting process for you since it forces you to think about what you really want to study: spending 5 months on a focused subject really requires that you are interested in it. It also encourages you to visit labs, interact with researchers and learn what they are doing and for what reasons. Here are a few tips to help you in your lab hunt. Bottom line : meet with researchers, talk to their students, ask themquestions and visit their labs.

• Some tips to find an internship- Going through the list on the AIV’s website (there are internship offers posted regularly. You can also explore the internships that were done the previous years).- Searching on the websites of Universities and Institutions for a team or an unit according to your interests.- Speaking with FdV students and other students that come to the CRI and may know of interesting internship opportunities.- Typing key words (HIV, Paris) in Faculty 1000... A lot of labs have a good opinion of the master AIRE, so you should not have troubles with finding one. You can count on the AIRE team and plenty of others (us! aka past M2 students) at the CRI to help you to find your dream-internship.

As soon as you find a lab that could be interesting for you, write a mail to the PI. It should be short, direct, but personalized. Why are you writing? Who are you? Why are you writing to this lab in particular (the shorter the better, you can not be a spe-cialist after reading the abstract of the project on the website...) What do you expect from this internship? You can also asked the AIV team to write an official letter explaining the AIV master characteristics so that you can join it to your mail.

You are more important (for yourself ) than any Principal Investigator (PI), labora-tory or scientific project. So first, think about your priorities. Choose your internships based on them. For example, if during this year you want to learn the maximum and do it having fun, think about 3 totally different labs and be sure that you get along with the PI and with the team. If the atmosphere is bad, nobody will tell you (or rarely) “don’t come here !”, but if people are not saying “we are having a great time here, we love our lab”, it might be an indication....

The more labs you visit the better for you! It means experience in interviews, networ-king, learning a lot about what is happening in Paris science, tuning what you want, need and appreciate!

• Tips on how to contact the lab1. Keep in mind that good labs get many applications for internships. Therefore you should personalize your request and put the name of the person you want to contact in the first line.2. Read what they have done previously and explain what particular part of their work you like most. Give all the details about when will the internship take place (i.e. full

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time, 5 month starting February), describe any particular experiences you have and your motivation. Write a straightforward, short email.3. Attach a CV, giving information about your background, possible lab techniques you Master, programing skills...4. Ask them if you can meet them and visit their lab, specially if they are located in the Paris region.

As we already said above, the important point is to take time to search for a lab in which you will be confortable/feel great during the three months and have a real interest in the project.

•What do I have to ask before choosing a lab?The important point is to take time to search for a lab in which you will be confor-table/feel great during the three months and have a real interest in the project.

Ask if on the occasion of the interview you could come and spend a few hours to meet your advisor but also the team. Ask questions about their work and habits in the lab. Especially if there are PhD students or other master students in the lab, speak with them, they will be able to present you the lab and the environment with a dif-ferent point of view than the one of your (maybe future) supervisor. If a member of the CRI/AIV/FdV has already worked for the lab, we strongly advise you to ask him about his experience. Bad internships happen, unfortunately...

Don’t hesitate to request precisions on what you will do during those 3 months. It might be a good idea to ask the PI for a written schedule with some concrete expe-riments and tasks. If you ask for help or opinions at the CRI (never hesitate to do it), this written project will help your advisers. It could also serve you to asses how is going your internship...

It is important to ask during your interview about plans of the lab/PI to take a PhD student next year. Don’t feel obliged to promise anything during the interview and don’t expect the PI to promise you anything neither.

Don’t forget to introduce in your discussion the question of the remuneration. Some labs (fortunately not the majority!) accept to take you as an intern but are not able to pay you; in this case, you cannot accept their offer and will have to find another internship. It is indeed illegal for you to perform an internship for free. See the In-ternship section of the M1 chapter for more details.

There is a lot of great “extra-master” courses at the CRI. Have a look on them before starting the internship, if there is something you would like to follow, ask your PI if it is OK for him/her if you assist to a course during the internship. The dates or at least the amount of hours are known very early in the year.

• What your PI should knowYou will not come to the lab on Fridays afternoons, as you will have the AIV courses (Starting at 15h usually). This should be clear from the beginning for your advisor.

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Also, you will have an extra load of work when it’s your turn to present at CARA, BibSyn or ZOIO and you will certainly spend less time or be less efficient in the lab at this period. Make sure that your PI knows this from the beginning.

• When do I have to start looking for my internships?As soon as possible as your first experiment will normally start mid-September! So in practice you have to find a lab during the summer and start the administrative process end of august, beginning of september. For the second and third internships, you should have found a lab, typically one month before the starting date to let some time to the university administration to process your files.

• Why the first and second internships are so important?- If you think about doing your PhD in France, the most important of your intern-ships could be the first one, as PIs are searching quite early for candidates (they want to test you but also you want to test them!). The optimal situation is to do your first internship in the lab where you would dream to make your PhD. Then you’ll have a “sure” position and you can start to work on your PhD project early.

- Interviews for PhD internships are extremely competitive. The better you know the team and the project, the better for you. Of course it is possible to prepare a presen-tation on a PhD project in two weeks, but it will surely be more difficult and stressful than having few months.

- Some french doctoral schools ask to submit the PhD projects in the beginning of January. This is done by the PI, but not all the PIs do it systematically every year. So if you want to do your PhD in the lab and the PI has the possibility to take a PhD student next year, be sure that he or she submits your project on time.

- As you will see, during the M2 year, time is going really fast. If you know early in which lab you want to do your PhD you will be able to apply for more fellowships (AXA, universities...)

- If the PI wants a PhD and your first internship turns to be a great success: perfect! If something tells you that you should not stay in a particular lab for your PhD you have a second shot.

- Don’t be afraid reading this part if you still don’t know for the moment if you want to do a PhD and where you would like to do it. If you decide in February or March it’s still good. But it’s true that “positions” are being occupied fast and you might have a strongly reduced choice of labs proposing a PhD if you start searching in April... The important thing to keep in mind is that you have to be sure that this is The lab for you which depends on your priorities!

• What if I don’t have much experience/knowledge in the subject of my internship?It is not an obligation to have experience and knowledge on the subject of your internship, which means that you can apply for internships that you’re interested in even if you don’t have a solid background in that area. You’ll be able to learn a

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great deal during these kinds of internships, so don’t be afraid to explore new areas of research ! Make sure that you state from the beginning your level of knowledge and of course show your motivation ! Some labs will gladly take you in, especially if they work on an interdisciplinary project and are accustomed to a mix of different backgrounds.

• Internships are paid !In France, lab rotations are regulated by law. The laboratory in which you will perform your internship has to sign a binding agreement with the university you are registered to before you can start to work. It is a rigid and slow system since many different actors have to sign the same document in four copies. These documents are available on the websites of Paris Diderot and Paris Descartes universities and on the Moodle (http://www.moodle-cri.org/course/view.php?id=318).

Once you found a research team that is willing to host you, you should download the form, fill it in, sign it and give it to your lab for signature. This document should then be given to the AIV secretary for signature. After, it will be then sent to the university you registered to (Paris Descartes or Paris Diderot). The whole process usually takes a month, so it’s a good idea to start in advance. It is also required for international internships and it takes even longer to get the signed document, so be responsible and start early.

On the good side, this internship agreement («convention de stage») will allow you to work in safe conditions: you’ll be protected by the university insurance in case something occurs, you being injured or you being at the origin of a massive fire, for example. Such things usually don’t happen, but it’s better to be covered.

The other good news is that you will be paid for your internship, if it is done in France. The French law is very clear on that subject: any internship lasting longer than 2 months (regular working days and hours) must be paid by the team hos-ting you. You will not be paid a full salary, but a compensation of typically 450€ a month for your work. This is not something negotiable and you should run away from labs that are reticent to pay you for your work and propose you to sign seve-ral one month internship agreement or other weird alternatives. Such proposition are illegal anyway. Importantly, the universities will not sign the «convention de stage» if the lab refuses to pay you. It’s a recent law (2010) and some researchers are not yet fully aware of it. If you have any doubts or problems related to this issue, please let us know as soon as possible.

• Doing an Internship abroad / Away from Paris?

It may be possible to do an internship outside of Paris, in France or abroad. If you are planning to do so, please come discuss with us what you have in mind as soon as possible. We prefer to keep students around Paris so that they can interact and meet every week during the seminars and scientific communications sessions, but if you can convince us that it’s best for you to go abroad for your internship, then we’ll try to help you as much as we can. For the M2 students, the first internship

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must be done close to Paris, since we want you to be with us for the first semester and enjoy the different group work and socialization events. Unfortunately we won’t be able to support you financially, so you’ll need to find a fellowship or ano-ther way to pay for your travel expanses. When you are abroad, we will ask you to follow the classes using the moodle, to keep contact with us, and to follow semi-nars or courses to your host university in order to compensate for the classes that you will missed.

Concerning funding, Paris Descartes and Diderot Universities propose a “Mobi-lity Fellowship” on social and education criteria. With this single application, you can get money from either Erasmus, Région Île-de-France or University. If you are lucky, you will get a maximum amount of 450€/month... which helps a little bit to live abroad. For accommodation and extra-funding, you should negotiate with your hosting lab.When doing an internship abroad, or far from Paris, you will be asked to partici-pate to the Moodle, to come back for your presentation and to take extra courses to the university your lab is attached to, in order to compensante for your absence

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Master AIRE

Centre de Recherche Interdisciplinaire8-10 rue Charles V

75004, Paris.