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Master AIRE
Approches Interdisciplinaires de la
Recherche et de l’Education
2014-2015
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Master AIRE
Centre de Recherche Interdisciplinaire
8-10 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...
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Contents
General Information 7
1.  M1 / AI 11
1.1 General Information  11
1.2 The content of the first year (M1) 11...
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The AIRE Master is designed to help you find your way in research and design
yourprofessionalcarreerinscienceandedu...
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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 organi...
APPROCHES INTERDISCIPLINAIRES DU VIVANT
INTERDISCIPLINARY APPROACHES TO LIFE SCIENCES
AIV
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AIV/M1
1.  M1 / AI
1.1 General Information
ThefirstyearoftheMasterisdesignedtoteachprimarilysyntheticandsystemsbio...
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focusmoreonthemathematicalandphysicalconceptsthatareusedinquantitative
description of living systems.
After this b...
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AIV/M1
•  Second Semester (February - July)
The second semester will focus on practicing research. You will spend ...
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•	 Deadline for internship «convention de stage» - 15/12.
•	 First semester exams - 17/12 (Exp methods); 15/12 (Dy...
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AIV/M1
•  Matlab programming project
During the third week, you will work by groups of two students on a Matlab pr...
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Greenhalgh(http://www.tcnj.edu/~library/gorman/How-to-read-a-paper.htm)and
DG Altman (http://www.medcalc.org/liter...
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AIV/M1
Alon 2007
The course will be based on and/or inspired from many other papers that will be
made available (b...
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http://www.nature.com/nature/comics/syntheticbiologycomic/
•  Computational Biology, Main module
«Instilling in st...
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AIV/M1
•  Computational Biology: Rule based Modelling
Teachers:VincentDanos(vdanos@inf.ed.ac.uk),JérômeFeret(jerom...
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cal concepts as well as technical skills.
Deadlines: to be announced
Overviewoftheclass:Wewilladdressthesubjectfro...
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AIV/M1
Requirements:Totakemaximaladvantageoftheclassyoushouldhaveageneralidea
of programming, ideally in the Matla...
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3. What makes MTs stiffer than actin filaments.
4. How cytoskeletal filaments are organized the way they are in ce...
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AIV/M1
with a schedule for the next days of experiments and precise protocols. There will
then be four full days p...
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whichcommunicationskillsplayamajorrole:writingpapers,readingpapers,giving
seminars,discussingwithcolleagues,commun...
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AIV/M1
legg (Eds), Practising Science Communication in the Information Age: Theori-
sing Professional Practices, T...
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1.6 What’s next ?
AttheendoftheMaster1,andgiventhatyouhavepassedallexamswewilldiscuss
with you the opporunity for ...
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AIV/M2
2.  M2/AIV
2.1 Content  Planning of the year
The year starts by a one week workshop at Sèvres and then stud...
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»» To learn how to write a research proposal.
»» To discuss scientific questions thoroughly.
»» To learn to intera...
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AIV/M2
2. All students participating in the session have to add their comments at theWork-
placeentry(followinstru...
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4.Includea discussionofoneemergingopenquestionarisingfromtheirreviewand
present detailed experimental/modeling app...
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AIV/M2
gly. If you do not agree - prepare to defend your point of view.
(iv) An editorial board will be formed by ...
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2.3 Who to contact ?
For general enquiry about the master, please do contact the secretary during the
opening hour...
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AIV/M2
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FOSTER
Formation pour l’Ouverture des Sciences, des Technologies, de
l’Education et de la Recherche
Fostering Open Science...
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Foster/M1
3.	FOSTER/M1
3.1 General Information
The first year of the Master is designed to teach the basics of a t...
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UE1 --- Serious Games (A. Taly)
UE2 --- Learning by doing (J. Chevrier)
UE3 --- Science Communication (JM. Galan)
...
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Foster/M1
ofallstudentsismandatory.Seetheinternshipsectionattheendofthisbookletfor
more details and advice on how ...
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and tools that can help you to test and build your ideas throughout the year.
•  Computer programmation : Python /...
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Foster/M1
Goaloftheclass:Thebestwaytounderstandthemeaningofwhatyoulearnandto
beabletocreateistodoitbyyourself.Inth...
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Goal of the class :Why « Innovation » is now matched with « education » ? Students
willconductanhistoricalapproach...
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Foster/M2
4.  FOSTER/M2
4.1 Content  Planning of the year
The organization of the year is rather simple: it starts...
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•  Review on Pedagogical Innovation (REPI)
validation: group work, reading, report, presentation
Theaimoftheworksh...
INTERNSHIPS
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Internships
5.  INTERNSHIPS
Findingalabthatfitsyourresearchinterestusuallytakessometime,bothtorespect
theadministr...
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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...
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Internships
time,5monthstartingFebruary),describeanyparticularexperiencesyouhaveand
your motivation. Write a strai...
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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 cert...
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Internships
great deal during these kinds of internships, so don’t be afraid to explore new areas
of research ! Ma...
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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 ...
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Internships
Master AIRE
Centre de Recherche Interdisciplinaire
8-10 rue Charles V
75004, Paris.
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Master AIRE 2014

Master AIRE, Approches Interdisciplinaires de la Recherche et de l’Education 2014-2015

1- Master Approches interdisciplinaires du Vivant / Interdisciplinary approaches to Life Science.

2- Master 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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Master AIRE 2014

  1. 1. Master AIRE Approches Interdisciplinaires de la Recherche et de l’Education 2014-2015
  2. 2. 2 / 54 Master AIRE Centre de Recherche Interdisciplinaire 8-10 rue Charles V 75004, Paris.
  3. 3. 3 / 54 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 startedtheyearandmetyourfellowstudents.Thisguidewillsum- marizemostofthecoursesandopportunitiesofferedbyourpro- 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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  5. 5. 5 / 54 Contents General Information 7 1.  M1 / AI 11 1.1 General Information 11 1.2 The content of the first year (M1) 11 1.3 Planning of the Year 13 1.4 Details of the Courses 14 1.5 Who to Contact ? 25 1.6 What’s next ? 26 2. M2/AIV 27 2.1 Content Planning of the year 27 2.2 Details of the course 27 2.3 Who to contact ? 32 3.  FOSTER/M1 35 3.1 General Information 37 3.2  The content of the first year (M1) 37 3.3  Planning of the Year (2014-2015) 39 3.4  Details of the Courses 39 3.5  Who to contact? 42 4. FOSTER/M2 43 4.1 Content Planning of the year 43 4.2 Details of the course 43 4.3 Who to contact ? 44 5. INTERNSHIPS 45
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  7. 7. 7 / 54 The AIRE Master is designed to help you find your way in research and design yourprofessionalcarreerinscienceandeducation.Youwillhavetheopportunityto learn what research is, to get a lot of practical experience in labs and companies, to meetwithmanyresearchersandtodiscussrecentinterdisicplinaryresearcharticles 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 withus,withtheotherstudents,toparticipatetoextracurriculumactivitiessuchas the CRI scientific clubs.You can also organize events, create or participate to scien- tificclubs,inviteresearchers,etc...Beinvolved,shareyourknowledgeandexpertise 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 radicalydifferentbackgroundthanyou.Theideaisforyoutoshareyouknowledge, todiscussaboutscience,toconfrontyourideas,eitherduringthefridayssessionsor duringtheclubs.Becreative,don’tbeshyandtrynewthings,ornewprojects.Ifyou 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 worthtryingagainandagain.Asaruleofthumb,ifyoudon’tunderstandsomething, just ask ! 3 - Come prepared. Read the, course materials, the article or the reviews several timesbeforetheclasses.ParticipatetotheMoodle,engageindiscussionbeforeand 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
  8. 8. 8 / 54 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,youareallexpectedtoattendatalltime,andnotonlyforyourtalk,whichis very disrespectful for your colleagues. Alsoandimportantly,weencouragecreativity.Youcanorganizeevents,createorpar- ticipatetoscientificclubs,inviteresearcherstoattendtothefridaysessionsorgivea talk, etc... Be involved, share your knowledge and you will spend a very interesting, rich and entertaining year with us.
  9. 9. APPROCHES INTERDISCIPLINAIRES DU VIVANT INTERDISCIPLINARY APPROACHES TO LIFE SCIENCES AIV
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  11. 11. 11 / 54 AIV/M1 1.  M1 / AI 1.1 General Information ThefirstyearoftheMasterisdesignedtoteachprimarilysyntheticandsystemsbio- logy.Youwillalsobetrainedincomputerscience,statistics,experimentalmethods, biophysicsandmoregenerallyonquantitativeapproachesinlifesciences.EachAIV yearclassbringsit’snovelmixofbiologists,computerscientists,physicistsandengi- neers.Thisdiversityinacademicpathsisanexceptionalopportunityforyoutodisco- 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 meanstoprepareallcourses,inparticularbyreadingsciencearticles,toaskquestions when you don’t understand something and to be proactive in classes.You are pro- bablyalreadyregisteredtoouronlineteachingplatformcalledMoodle.Thisisavery powerfultoolandyou’llhavetouseitforpracticallyeverycourse.Teachingmaterials (articles,PDFs)willbepostedbytheteachersforyoutoreadandthinkonbeforethe 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. ThespiritoftheMasteristoresponsabilizethestudentsandtomaximizeexchanges amongst them. As a result it is crucial that you attend all courses. Students are also expectedtobeontimeandtorespectdeadlines.Ifyoucannotcometoacourse,let the teachers know about it beforehand. Similarly, if you feel that you are not going tobeabletomeetadeadline,orifyouhaveaproblemwithacourse,doletusknow assoonaspossible.It’smucheasiertofindasolutionifweareawareoftheproblem in advance. 1.2 The content of the first year (M1) •  First Semester (September - January) Thefirstsemesterstartsbya3weekslongbootcampthatgivesacondensedoverview 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 thesubjectsthatwillemergeduringthesemester,andtogiveanintuitiononwhich subjects the students should start working on their own. Typically, a student with physicsbackgroundneedstoworkonfundamentalbiologicalconceptssuchascen- tral dogma, evolution, DNA, methods in biology, while a biologist usually needs to
  12. 12. 12 / 54 focusmoreonthemathematicalandphysicalconceptsthatareusedinquantitative description of living systems. After this bootcamp, several core courses will take place every week.You will learn thetheoreticalandpracticalconceptsthatarerequiredtoperformscientificresearch 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.Gradeswillbebasedonyourattendance,oralparticipationinclasses,quality of your homework and success to the final exam. Although you need to validate 6 coursesoverthe8thatareproposed,wedoexpectyoutofollowallcoursesandpass all exams. For your final grades, we will keep the 6 best ones. Regardingthegrades,pleasedonotethat,bydefinitiontheirmeaningisverylimited - what does that really mean to have 14/20 to an exam? How much does that tell aboutyourskillsanddeepunderstandingofascientificdomain?Thisiswhywewill also provide you with a written evaluation, detailing what are your strong skills and inwhichaspectsyoushouldimproveforeachcourses.Wewillalsoprovideyouwith mid-termoralevaluationthroughaninformalandinteractivediscussionbetweenthe 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 eitherTimo Betz (Monday morning), or Pascal Hersen (Friday morning) will offer time to help you in scientificandacademicproblems.Pleasecheckthescheduleforthedatesandcontact the teachers at least 3 days before the sessions with possible questions you have. Furthermore,wehaveimplementedamid-termexam,whereeachstudentwillhave 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 studentsshouldbewellprepared.Incaseofinsufficientknowledge,studentswillhave to follow extra coursework to ensure best results in all the classes.
  13. 13. 13 / 54 AIV/M1 •  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) Bothclasseswillbeevaluatedbasedonyourattendance,oralparticipationandori- ginal contributions. •  Research Internship (February - June) Theresearchinternshipisanintegralpartofyourtraining.Theinternshipwillbefull 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 theendofJune,butthiscanbesubjecttoindividualchangesaslongastheinternship lastsatleast5month.Anyresearchprojectsrelatedtosynthetic,systemsandquanti- tativebiologyarepossible.Itisagreatopportunityforyoutodiscoverwhatitactually meanstodoresearchinalaboratory.Seethedetailsonhowtofindaninternshipat 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 andparticipatetothiscompetitionofsyntheticbiology.Thisusuallystartsbybrains- tormingsessionsandprojectbuildinganddoesnotrequireafulltimeinvolvement 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 finaletakesplaceinNovember,youwillhavetoorganizeyourselftostayintheteam uptothatdate.ForthoseofyoucontinuingwithusinthesecondyearoftheMaster, this means that your first lab rotation of M2 will be dedicated to finishing the iGEM team project. 1.3 Planning of the Year Youcanconsulttheyearagendaonthewebsite.Someofthedatesmaychangesodo 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 November
  14. 14. 14 / 54 • 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 probablynewandcomplicated.Luckily,youareaninterdisciplinarycrowd,sothere shouldbealwayssomeoneclosetoyouthatmightbehelpful.Thisisoneofthemost 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 conductingashortbibliographicprojectinbiology,aprogrammingprojectinMat- 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.Thisisagreatopportunitytogooversomebasicbiology,help yourcolleagueswhomaybefromadifferentfieldtopickupsomebitsthattheymay bemissing,andparticipateincreatinganinterestingeducationaltool.Youwillwork in groups, and the hope is that your work will be published on the Science website, along the annotated articles that are already there.
  15. 15. 15 / 54 AIV/M1 •  Matlab programming project During the third week, you will work by groups of two students on a Matlab pro- grammingproject.Thegoaloftheseprojectwillbetowritea(fun)gameora(useful) imageanalysisprogram.Therewillbedifferentdegreesofcomplexityfortheprojects tomeetthedifferentlevelsofthestudents.Youwillbeaskedtodocumentyourwork 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(jean-christophe.thalabard@htd.aphp.fr) Hours: 7 Sessions, each for 3 hours Evaluation: Active individual participation at each session is the basis of the final Validation: At each session, 2 or 3 groups of 2-3 students present an article. Each studentissupposedtoparticipatetoatleast2oralpresentationsandbeingactively involved in the discussion of the presentations from the others. Deadlines:Eachpresentinggroupprovidesitssupportingsetofslidesatthetimeof its presentation. Overview of the class: In the land of the monolingual: «Translating a basic finding intoanewtherapyrequiresustospeakmanylanguages-scientific,clinical,legaland financial.Yet most of us are hopelessly monolingual, a limitation that substantially slowstranslationalresearch.Stepshavebeentakentoaddressthisproblem,butalot 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 discussingperse.Articleswillbeselectedinordertocovervariousaspectsofclinical research,fromearlyreportofbiotechnologicaland/ortherapeuticadvances,innova- tivedesignstometa-analysisofpublishedresultswhenthetimehascometoglobally 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 articlesarestructuredandmoreimportantlydiscussed;ii)tosummarizeandpresent the results of both original and review articles in the medical field. Requirements:noformalpreviousknowledgeisrequiredinthiscourse,althoughan activereadingoftheproposedarticleswilltakeadvantageofnotionsinbiostatistics, experimental design, but also epistemology and various approaches to causality. Suggested reading:Two series of short articles published in the Br. J. Medicine byT
  16. 16. 16 / 54 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 (clement.nizak@espci.fr), Gabrielle Woronoff (gabrielle. woronoff@espci.fr), Dany Chauvin (dany.chauvin@espci.fr) 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 conceptsofstatisticalphysicsandengineeringthathavebeenverysuccessfulinsol- ving such problems in other disciplines. We will then show how they apply to the descriptionofbiologicalsystems.Theexampleswewillcoverspanfromthemolecular to the ecological scale, and will include i) self-organized subcellular systems, ii) cell functionssuchasregulationofproteinexpression,divisionandcircadiancycles,and metabolism,iii)multicellulardevelopmentregulation,iv)evolutionofbio-molecules, cells, multicellulars and populations, and v) ecosystems. The course will be groun- dedonquantitativebiologyandmodelingbutwillalwaysbemotivatedbyexamples coming from biological systems. Goals of the class: 1.Tobecomefamiliarwithbasicconceptsandmodelsofstatisticalphysicsandengi- 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:thebootcampwillbeanidealpreparationtothiscourse,thereareno 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
  17. 17. 17 / 54 AIV/M1 Alon 2007 The 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:JakeWintermute(ehwintermute@gmail.com),IanMarcus(ianmmarcus@ gmail.com) Hours: 12 Sessions of 4 hours plus a final oral presentation in early January. Evaluation:Thecoursegradewillbein3parts.1/3Ateampresentationonarelevant paper. 1/3 Several brief written reviews of the literature and quantitative exercises. 1/3 The final project and exam. Deadlines:ThefinalexaminearlyJanuarywillincludeateampresentation.Anexact date will be set as early as possible in the semester. Overviewoftheclass:SyntheticBiologistsworktodesignandcreatebiologicalsys- 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 uncleardefinition,vagueboundaries,andboundlessambition.Wewillwrestlewith uncertainty, diffused information, conflicting intuitions and multi-disciplinarily. Coursegraduateswillbepreparedtodesigntheirownmade-to-ordersystems,and will be familiar with the lab techniques required to bring them to life. The course includesnolaboratorycomponent.Itisideallycomplementedbyawetlabrotation in molecular biology or participation to the iGEM competition. Goaloftheclass:Graduatesfromthiscoursewillbepreparedtocreatelivingthingsof theirowndesign,andtoanswerthefollowingquestions:HowdoesaDNAsequence becomeworkinggene?Howcanyoucreatecomplexfunctionswithmultiplegenes? 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 studentswillbetotallycomfortableinbothsubjects.Thereforewewillprovideaccess 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.
  18. 18. 18 / 54 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 (gregory.batt@inria.fr) and Dusan Misevic (dule@alife.org) Hours:12sessionsof4hoursplusafinaloralpresentationinearlyJanuary.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:Deadlineswillbeassignedtothetwopracticalreportsduringthesemes- ter and to the final exam’s report as early as possible in the semester. Overviewoftheclass:Usingnovelexperimentaltechniques,quantitativedatacanbe 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- basedapproach:modelsareproposed,analyzedandcomparedwithrespecttoexpe- rimentaldata.Usingmodels,variousassumptionsonbiologicalmechanismscanbe corroboratedorinvalidatedbytheexperimentaldataonarationalbasis.Experimen- tally-validatedmodelscanthenbeusedtomakenovelpredictionsororientsystem design.Theobjectiveofthiscourseistointroducethemodel-basedapproachofbio- logicalsystemsanalysisfromapracticalpointofview.Theemphasiswillbegivenon the modeling work, and on simple but important analysis methods. Such methods includestatespaceanalysis,globaloptimizationforparametersearch,andsensitivity analysis for robustness assessment. Goals of the class: 1.Testingtheconsistencyofquantitativedataproducedinlabsandcurrentunders- tanding of the functioning of the observed process 2. Basic understanding of modeling: how to represent reality using mathematical notions 3. Basic skills of analysis: numerical simulation, robustness, parameter search 4. Notions on how to model biological variability Requirements:Thiscourseismadeforpeople*not*familiarwithbiomolecularpro- cess modeling, dynamical system analysis, or Matlab programming.The sole requi- rementsarethereforeelementarycalculusandnotionsofmolecularandcellularbio- 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 -Modelingandsimulationofgeneticregulatorysystems:aliteraturereview,byH.de Jong, Journal of computational biology, 2002
  19. 19. 19 / 54 AIV/M1 •  Computational Biology: Rule based Modelling Teachers:VincentDanos(vdanos@inf.ed.ac.uk),JérômeFeret(jerome.feret@ens.fr), Jean Krivine (jean.krivine@pps.univ-paris-diderot.fr) 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 Overviewoftheclass:Inthisclass,youwilllearnanewway,calledrule-basedmodel- ling,toperformmechanisticmodellingwhichisverydifferentfromthatofthemore usual approach through ODEs.This approach builds models by writing,in a simple formal language called Kappa, rules that describe directly the possible interactions betweenproteins;thesemodelscanbeequippedwithratelawsandthensimulated andanalyzedwithopensourcesoftwaretools(thatwewillprovide).Theclassispri- marilypracticalwhereyouwilldevelop,thinkaboutandanalyzeaseriesofincreasin- glycomplicatedsystemsusingKappa.Thereisalsosomepurelecturingtimeinorder 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 abouthowsignallingnetworksoperate.Theuseofrule-basedmodellingmakesiteasy totryoutvariantsofamodel,whichsometimeshaveverydifferentbehaviour,andso thereisastronglyemphasisonexploratorylearning.Youwillalsolearnsomespecific technicalmaterial,notablyaboutstochasticsimulation,thatcomplementswhatyou 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 andexecutingmodelsandsomebasicintuitionsaboutprobabilitytheorywillhelpfor 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:10sessionsof4hourseach(2hoursteachingand2hourspracticepersession) Evaluation:Thefinalgradewillbedeterminedonthebasisofactivitiesdevelopedin thecourseandalsoonafinalexam.Evaluationwillassesstheassimilationofstatisti-
  20. 20. 20 / 54 cal concepts as well as technical skills. Deadlines: to be announced Overviewoftheclass:Wewilladdressthesubjectfromtheperspectiveofinference. Inthebeginningofthecourse,wewilloverviewanddiscussdescriptivestatisticsand poll-basedexperimentstomotivatetheneedforaprobabilisticmodellingframework anddevelopafeelingforstatisticalreasoning.Then,wewilldiscusscommonlyused methodsofestimationandhypothesistesting(e.g.comparisonofmeans,linearre- gression,analysisofvariance),basedonrigorousbutsimplemathematicaldevelop- mentsandemphasisonconceptualissues,andworkontheirapplicationtoexample problems in the practical sessions. Goaloftheclass:Firstaimistodevelopthestudents’criticalthinkingfortheconnec- tionbetweenstatisticalreasoningandreal-worldproblems.Secondaimisenabling studentstodetermineappropriatemethodsfortheanalysisofdifferentdatasets,star- ting from a toolkit of common inference techniques. Requirements: Calculus (including integration) •  Dynamics of Living Systems Teachers: Emmanuel Farge (emmanuel.farge@curie.fr), Timo Betz (timo.betz@ curie.fr), 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. Overviewoftheclass:Whileyouwilllearninmanyotherclassesthetheoreticalfoun- dationsofcomplexsystems,youwillbeabletoapplythesenewlyacquiredknowledge inthisclass.Themainideaistoprovideyouwithasetofpreviouslypublishedpapers, eachdescribingadynamicalprocessthathappensinlivingsystemssuchasdevelo- pingorganisms,tissuesorthesinglecelllevel.Eachofthesepaperscombinesexpe- rimentalknowledgewithamathematicalmodeltounderstandthecomplexsituation itdescribes.Toreproducetheexperimentaldata,themathematicalmodelsareclosely investigatedinacomputersimulation,andonegoaloftheclassistoreproducethese 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. Goaloftheclass:Understandingacomplexmathematicalmodelofabiologicalpro- 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 constructivecriticism.Developyourindividualwaytoimprovepreviouslypublished work.
  21. 21. 21 / 54 AIV/M1 Requirements:Totakemaximaladvantageoftheclassyoushouldhaveageneralidea 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 (minc.nicolas@ijm.univ-paris-diderot.fr ) , Guillaume Ro- met-Lemonne (romet@lebs.cnrs-gif.fr) 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 students Evaluation: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-talkbetweenphysicalandbiologicalmechanismsintheregulationofbasicbio- logicalprocesses.Thecoursewillparticularlyfocusonthecytoskeletonanditsimpact oncellgrowth,polarity,morphogenesisanddivision.Halfofthecoursewillbededi- catedtointroducebasicsofmicrotubulesandactinregulationandtheotherhalfwill focus on discussing examples that underlie their role in different cellular contexts. Thiscoursewillservetointroducebasicprinciplesandanoutlookofmoderntoolsin biophysicsasanintroductiontotherealexperimentalcourse.Keyquestionthatwill beaddressedinclude:howdocytoskeletalelementsgenerateforces?Howarethese forcesintegratedbycellstopositionorganellesorgeneratecellular-scaleforces?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 techniqueswillbediscussed.Itwillhighlightdifferencesbetweencelltypes,biologi- calscalesandconserveddesignprinciplesorrules.Studentswilllearntoobserve,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.
  22. 22. 22 / 54 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 positioning 7. Orders of magnitude and scaling concepts of cytoskeleton mechanics in cells 8. Mechanisms and mechanics of cytokinesis 9. Cytoskeleton and cell shape determination Requirements:Totakemaximaladvantageoftheclassyoushouldhaveabroadidea 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 2005 Kirschner 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 (matthieu.piel@curie.fr), Anne Paoletti (Anne.Paoletti@ curie.fr) 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 understandingofthemethodsyouhaveusedinyourproject,soaskquestionsonhow things work and listen to the answer! Overviewoftheclass:Duringthisclassyouwilldesign,executeandinterpretexperi- ments.Therewillbeseveraltypesofexperimentsproposed,allsharingonecharacte- ristic:thereisaquantificationbasedonimaging,thendataanalysis.Youwillusethe fissionyeastS.Pombeasamodelorganismanddesignquantitativeexperimentsto 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, throughanexperimentalapproach.Thequestionhastowellformulated,theexperi- mentswelladaptedtoansweritandtheresultwellinterpreted(withitslimitations). Bylettingyou,asmuchaspossible,designtheexperiments,runthemandinterpret 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 willspendanafternoondesigningexperimentsindetails,withthegoaltocomeup
  23. 23. 23 / 54 AIV/M1 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 bedone,fromafirstsetofanalysis.Extracteddatawillthenbefurtheranalysedand interpreted,goingbackandforthbetweenexperimentsandanalysisuntilthereare enoughdatatoreachaconclusion.Eachgroupwillshortlypresentitsresultsanddis- cusstheminthelastsession.Thegoalofthislastpartistojudgewhetherthewhole processledtoaninterestinganswerornot,andtodiscussaboutthenextstepstotake 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,butyouneedtohavesomebackgroundknowledgeonthebiologyandthe physicsinvolved.ThiswillbeprovidedduringthecourseorganizedbyNicolasMinc 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-dependentcellmorphogenesisinthefissionyeast.MartinSG.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. -Physicalmechanismsredirectingcellpolarityandcellshapeinfissionyeast.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 sessions Marks: The evaluation is based on three criteria: the participation to the class dis- cussionsandflash-workshops;thedeliveryofa10minutespresentationwithvisual supportsonthesubjectofthestudentinternship;therealisationofagroupprojectof public science communication. Deadlines:Thescientificpresentationisdueatmidterm(after4sessions);thegroup project is due at the one-before last class. Overviewoftheclass: Thecoursefocusesontherelevanceofcommunicationinthe various aspects of the scientific activity. It presents an overview of the communica- tionskillsnecessarywithinthescientificcommunity,aswellaswhenaddressingthe generalpublic.Infact,thereareagreatvarietyofactivitiesinthelifeofascientistsin
  24. 24. 24 / 54 whichcommunicationskillsplayamajorrole:writingpapers,readingpapers,giving seminars,discussingwithcolleagues,communicatingwithinalaboraworkinggroup, 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 bodyofknowledge.Therefore,thecoursefocusonhelpingthestudentstolearnhow tolearnfromtheobservationofcommunicationproductstheyencounterintheirlife (posters,oralpresentations,scientificpapers,popularpress,meetingsatthecafeteria, 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 tricks 4.Writing for scientists or for the general public: main differences and case studies. 5. Science in society and public perception of science 6. Science in the media, science and cinema, science museums, citizen science and publicparticipation,…(onetopic,dependingonwherethediscussionswillleadus) Besidesthisseriesoflectures,eachsessionwillincludespracticalexercises,specifically focusingonpeer-learningactivities.Inaddition,thestudentsareexpectedtoprepare oneten-minutespresentationonthetopicoftheirinternship,andonesciencecom- 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 • Acquiringobservationskills,i.e.,learningtoobserveotherscientists’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: • FrankBurnet,Whyandhowtocommunicateyourresearch(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-
  25. 25. 25 / 54 AIV/M1 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-Decemberatthelatest).Notthatitmaytakesometimetosignthisconvention, and you need it to start the internship. 4 - Start your internship on the 1st of February. •  Internship Evaluation At 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,resultsandperspectivesoftheinternships;oneschemedescribing 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 willbeabletoguideyouorputyouincontactwiththerightpersontohelpyou 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.
  26. 26. 26 / 54 1.6 What’s next ? AttheendoftheMaster1,andgiventhatyouhavepassedallexamswewilldiscuss 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 anotherMasterprogramthatismorespecializedandfocusonyourfavoriteresearch topic, we’ll help you to make the transition.
  27. 27. 27 / 54 AIV/M2 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 - 12/09 Internship I : 15/09 - 31/12. CRI Opening Days : 01-02/10 Internship I defense : 17-18-19 december Internship II : 07/01 - 05/04 Internship II defence : first week of april (joint event with FdV) Internship III : 15/04 - 15/07 Reharsal 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 andcommunicationthroughdialogueandbrainstormingonopenquestionsinLife 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
  28. 28. 28 / 54 »» 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 15:00 Remarks : Mandatory Validation : Mark10; 80% of active presence in seminars and comments contribu- tion in the workplace Course objective: Developthestudent’sabilitytoreadandcriticallyinterpretpapersfromhighquality journals.Throughthisexercisethestudentswillbeexposedtoalargespectraofinter- 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- ferentbackgrounds,presentingindetailaninterdisciplinaryresearchpaperoftheir choice.Theunderlyinghypothesis,backgroundandtheresultsisdiscussedindetail andthedifferenttechniquesexplained.Inaddition,thestudentsareaskedtosuggest furtherexperimental/modelingapproacheswithrespecttotheirconclusionsfromthe paperatstake.Allstudentsareexpectedtoparticipateinthecourseforum,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 thateverypairpresentersshouldputtheirabstractsandreceivecommentsfromALL 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 Organization 1.Atleast8daysbeforeeachpresentation,placeyourarticleinthe‘Workplace’with your own abstract placed in the forum; include hyperlink(s) to your entries to the database (including any Supporting Material).
  29. 29. 29 / 54 AIV/M2 2. All students participating in the session have to add their comments at theWork- placeentry(followinstructionstherein)nolaterthan3daysbeforethepresentation (e.g. Tuesday). 3. A Short debriefing of the presenters by the AIV mentors will take place after the seminarfocusingonthesciencediscussedaswellasonthequalityofpresentation.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-groupwilldebrieftheircolleagues(5-10minutes)aboutthesessiontheydidnot attend. 5.Postyourpresentationfile(pptorpdf),takingintoaccountthepost-presentation commentsinTheCARApresentationsdatabase(deadline:Monday.Writedownthe summary of comments received as post-evaluation. •  BibSyn - Bibliography Synthesis Format : 2 hours / week, Fridays at 15:00 Remarks : Mandatory Validation:Mark10;80%ofactivepresenceinseminarandCommentscontribution in the Workplace The course consists of a series of seminars, each initiated by two students from dif- ferentbackgrounds,presentingtheirreviewofscientificliteratureconcerningasub- 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.postingitinthedatabasetogetherwithwritinga200wordparagraphdescribing theresourceanditsrelevancetothereviewsubject.Thisshouldbedonenolaterthan two days before the presentation. Organization 1. 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.Presentaconcisereview,treatingtheirchosensubjectfromdifferentperspectives - their own as well as those raised in the forum. (1 hour including discussion). The slidesfile(pdf/ppt)shouldbesenttothetutors/teachersaweekbeforethepresenta- tion in order to receive their feedback!
  30. 30. 30 / 54 4.Includea discussionofoneemergingopenquestionarisingfromtheirreviewand 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 15:00 Remarks : Mandatory Validation: Mark10; 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-
  31. 31. 31 / 54 AIV/M2 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 Youwillhavetodothreeinternships.Youcanconsultthe«internship»sectionatthe 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 attendallthecoursesanseventsofthefirstsemester.YoucangoawayfromParis,but you need to be back in Paris for the courses every week. 2-TheSecondorThirdinternshipcanbedoneabroad.Thedurationofaninternship abroad is also of 3 months.The third internship can be, however, prolonged during thesummer. Incaseyougoabroad,youmustmakesurethatyouwillbethereforthe internship defense (early April, early July). 4-Wewillaskyoutoparticipatetothemoodleandtobebackforyourpresentation 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.
  32. 32. 32 / 54 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 Douady CARA : Anna Maria Lenon BibSyn : Danijela Vignjevic ZOIO : Olivia du Roure Internships : Pascal Hersen.
  33. 33. 33 / 54 AIV/M2
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  35. 35. 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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  37. 37. 37 / 54 Foster/M1 3. FOSTER/M1 3.1 General Information The first year of the Master is designed to teach the basics of a the future actors ofeducation.Philosophyoflearning,technologiesforeducationbutalsocognitive science and learning by doing, you will be trained in all the matters that form the coreofaninnovativeeducationthroughresearch.Beinvolved,shareyourknowledge andexpertiseandyouwillspendaveryfruitfulyear.Weexpectyoutoinvestalotof your skills and energy in the different courses.This means to prepare all courses, in particularbyreadingarticlesandbooks,toaskquestionswhenyoudon’tunderstand 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 thereforeimportantforyoutobeateasewiththistoolassoonaspossible.Notethat you’llalsobeevaluatedonhowmuchyouparticipated.ThespiritoftheMasteristo responsibilizethestudentsandtomaximizeexchangesamongstthem.Asaresultit 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,ifyoufeelthatyouarenotgoingtobeabletomeetadeadline, 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 youcommonknowledgeoncodingthatyouwillhavetousetodesignyourtoolsand 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 thetheoreticalandpracticalconceptsthatarerequiredtoactforopeningeducation technology, science and research..
  38. 38. 38 / 54 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.Gradeswillbebasedonyourattendance,oralparticipationinclasses,quality of your homework and success to the final exam. Although you need to validate 5 coursesoverthe7thatareproposed,wedoexpectyoutofollowallcoursesandpass all exams. For your final grades, we will keep the 5 best ones. Regarding the grades, pleasedonotethat,bydefinitiontheirmeaningisverylimited-whatdoesthatreally meantohave14/20toanexam?Howmuchdoesthattellaboutyourskillsanddeep 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- luationthroughaninformalandinteractivediscussionbetweenthemasterorganizers and the M1 student. •  Second Semester (February - July) Thesecondsemesterwillfocusonpracticalwork.Youwillspendatleast5monthsin aresearchlaborinacompany.YouwillalsohavesomemandatoryeventsattheCRI: UE2.1 --- Seminars UE2.2 --- Cognitive Science (E. Pasquinelli) Bothclasseswillbeevaluatedbasedonyourattendance,oralparticipationandpre- sentation. •  Research Internship (February - June) Theresearchinternshipisanintegralpartofyourtraining.Theinternshipwillbefull 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 researchresearcharepossible.Youwillhavetoturninashortreportcontaining:the projecttitleandthenameofyoursupervisoranditsaffiliation;anabstract(200-300) wordsdetailingbackground,objective,methodologies,resultsandperspectivesofthe internships; pictures, schemes or any visual representation of your activity are wel- come.UsuallytheoraldefenceisinthefirstweekofJuly,andyouwillhavetoturnin thereporttheMondayofthedefenceweek.Notethatattendancetothepresentation
  39. 39. 39 / 54 Foster/M1 ofallstudentsismandatory.Seetheinternshipsectionattheendofthisbookletfor 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 willdealwithit.IfyouareinterestedinthematteryoucouldbuildateamfortheCRI 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 maychangeduringtheyear,sodonothesitatetoaskusifyouhaveadoubt.Hereare 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.Whilesomeofthesubjectsmightbeeasyforyou,otherswillbeprobably newandcomplicated.Luckilyyouareaninterdisciplinarycrowd,sothereshouldbe alwayssomeoneclosetoyouthatmightbehelpful.Thisisoneofthemostimportant 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 Lhoste Discoverthepossibilitythatopentechnologygives.Arduinoisanopenhardware,it isoneofthewonderfultoolyoucanusetochangeyourenvironment.Easyofaccess 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
  40. 40. 40 / 54 and tools that can help you to test and build your ideas throughout the year. •  Computer programmation : Python / 22nd-26th of September Computerprogrammationisoneofthebasicseveryoneshouldlearn.Itiseverywhere inourworldandyoucannotdecentlyleaveittoasmallgroupofhightrainedcompu- terprogrammer.Whatismorecodingisawaytobetterunderstandwhatiseducation 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 createsomething.Eachdayyouwillhavetofacenewchallengesprogressingindif- ficulties one after the other. During this intensive week, you will have no obligation ofresultsbutweaskyoutogoasfarasyoucaneachday,tofacetheproblemandtry to solve it. •  FOSTER’S Ecosystem / 19th - 30th of September Education 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 whereyoucanfindthem.Youareinterestedinbuildingthefutureofeducationyou have to meet with these who change it now. • Léa Peersman-Pujol • Grégoire Serikoff • Ange Ansour •  Preparing the Opening days In 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 Taly Hours : To be determined Evaluation : 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 willcreateanoriginalgame.Asecondarygoalistointroducethestudentstoflipped 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-Pujol Evaluation : Project Presentation Hours : 3x6h in the lab, 2x3h to analyse the results, 26h to build your own project. Deadline : To be determined
  41. 41. 41 / 54 Foster/M1 Goaloftheclass:Thebestwaytounderstandthemeaningofwhatyoulearnandto beabletocreateistodoitbyyourself.IntheOpenlabstudentswilldiscoverscientific principlesthroughtheirownsenses.Withthatspiritofexperimentinmindtheywill be asked to design a project fitted to their own ambition. •  Science Communication Teachers : JM Galan, Simon Houriez, Cathy Dubois and Michel Avignon Hours : 20h of science communication lectures, 5h of case studies, 18h of science communcation towards death public. Evaluation : To be determined Deadline : 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, fromnewspaperstotwitter).Toenhanceyourcapabilitytoexpressspecificknowledge to specific public. •  Philosophy of learning Teachers : Antoine Janvier, Sophie Audidière, Robin Holmes, Stéfanie Masson Hours : 12h lectures, 9h reading, 19h workshop Evaluation : To be determined Deadline : To be determined Goaloftheclass:TheaimistounderstandthephilosophicalbasisofaXXIstcentury education.Through readings, lectures and workshops students will reflect on their ambition and projects for education. •  Technologies for learning Teachers : Sophie Pène, Jean-François Bonnet Hours : 10h of lectures, 40h of digital project building Evaluation : To be determined Deadline : To be determined Goal of the class : The students have to conduct together an whole digital project, includinguserexperiencedesign,technology,strategy,publishing.Theresultisaper- sonal portfolio and a cooperative learning MOOC. •  Pedagogical Innovation Teachers : Sophie Pène, Elie Sloïm Hours : 50h Evaluation : To be determined Deadline : To be determined
  42. 42. 42 / 54 Goal of the class :Why « Innovation » is now matched with « education » ? Students willconductanhistoricalapproach,acriticalanalysisandacontext-basedresearch. Wehopeenlightentheuseandthemeaningof«Innovation»(concept,management project, public policy…). Our aim is to describe the global EdTech (EducationTech- nologyServices)anditsexpansiontowardglobaldigitaleconomy,socialinnovation, changemaking,thesharingeconomy)withafocusontheMOOCandthenewissue of data driven improvement. •  Open Science Teachers : Salma Mesmoudi, Kilian Bazin, Cathy Dubois and Michel Avignon Hours : 43h Evaluation : To be determined Deadline : 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 handtorepresentdataandthecommunicationstrategycomingalongwith.toper- ceivethelinkbetweenscientificdataandsocietalchallenge(throughtheexampleof Haiti). To deal with citizen science, citizen mapping, benchmarking. •  Cognitive Science Teachers : Elena Pasquinelli Hours : 11 sessions- 32h Evaluation : To be determined Deadline : To be determined Goal of the class : To be able of propery using data produced by cognitive science. Tobeabletocollaboratewithcognitivescientisttoimprovethelearningprocess.To knowwhatcognitivesciencecanhelpyouwithandwhatitcannotdo.Tobefamiliar 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.
  43. 43. 43 / 54 Foster/M2 4.  FOSTER/M2 4.1 Content Planning of the year The organization of the year is rather simple: it starts by a one week workshop at Sèvresandthenstudentsareexpectedtoperform3internshipsofthreemonthseach 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 December Internship I defense : 17 of december. Internship II : 12/01 - 03/04 Internship II defence : first week of April, TBA (joint event with FdV and AIV) Internship III : 13/04 - 03/07 Internship 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 andresearchersfrombroadscientificbackgroundstoconceivecreativeprojectsatthe 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. • 
  44. 44. 44 / 54 •  Review on Pedagogical Innovation (REPI) validation: group work, reading, report, presentation Theaimoftheworkshopistobuildcriticalandcreativetools,todefineamethodolo- 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 Anypedagogicalinnovationisnotboundtobeworththepain,theaimoftheworks- hop is to understand the critical factors that can make it a success after you have determineditisusefultoyourgoals.Analysingdataandpreviousexperienceyouwill make these factors appears. •  Design, Creation and Evaluation of an Innovative Project (DECEIP) validation: group work, reading, report, presentation Hopefullywithourhelpandyourinternshipsexperience,youwilldeterminedapro- jectyouwouldliketoseehappenattheendorafteryourmaster.Thisworkshopwill help you design it deeply and build it. •  Internships Youwillhavetodothreeinternships.Youcanconsultthe«internship»sectionatthe 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 attendallthecoursesanseventsofthefirstsemester.YoucangoawayfromParis,but you need to be back in Paris for the courses every week. 2-TheSecondorThirdinternshipcanbedoneabroad.Thedurationofaninternship abroad is also of 3 months.The third internship can be, however, prolonged during thesummer. Incaseyougoabroad,youmustmakesurethatyouwillbethereforthe internship defense (early April, early July). 4-Wewillaskyoutoparticipatetothemoodleandtobebackforyourpresentation 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 ? ForgeneralenquiryabouttheMaster,pleasedocontactthesecretary,JulieCamonin, duringtheopeninghoursofthesecretariatorbyemail: Masterfoster@cri-paris.org. If you want to meet with us, ask us an appointment.We’ll be able to meet with you onWednesdaysbeforeorafterthesession.Forspecificrequestregardingonecourse, please do ask directly to your teacher.
  45. 45. INTERNSHIPS
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  47. 47. 47 / 54 Internships 5.  INTERNSHIPS Findingalabthatfitsyourresearchinterestusuallytakessometime,bothtorespect theadministrativedeadlinesandtomakesurethatyouwillfitnicelyinyourhosting 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,acompany,aNGO,etc...Thepedagogicalteamwillvalidateyourpropo- 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 tovalidateyourchoiceandtorecordtheactivityofourstudents.Thismeansthatthe adress,phone,contact,namesofyourlabsmustbeaccurate.Wealsoneedatitleand 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 sendyouanemailsayingthatyourinternshiphasbeenvalidated.Thiswillusuallybe 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 explainedbelow,thiscantakesometimesodothisassoonasyoureceivedourgreen 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 andtothejurycontaining:theprojecttitleandthenameofyoursupervisoranditsaf- filiation;anabstract(200-300)wordsdetailingbackground,objective,methodologies, resultsandperspectivesoftheinternships,visualrepresentationofatleastsomepart 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.
  48. 48. 48 / 54 •  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 youtovisitlabs,interactwithresearchersandlearnwhattheyaredoingandforwhat 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... AlotoflabshaveagoodopinionofthemasterAIRE,soyoushouldnothavetroubles 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- cialistafterreadingtheabstractoftheprojectonthewebsite...)Whatdoyouexpect 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- toryorscientificproject.Sofirst,thinkaboutyourpriorities.Chooseyourinternships basedonthem.Forexample,ifduringthisyearyouwanttolearnthemaximumand 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.... Themorelabsyouvisitthebetterforyou!Itmeansexperienceininterviews,networ- king,learningalotaboutwhatishappeninginParisscience,tuningwhatyouwant, need and appreciate! •  Tips on how to contact the lab 1.Keepinmindthatgoodlabsgetmanyapplicationsforinternships.Thereforeyou shouldpersonalizeyourrequestandputthenameofthepersonyouwanttocontact in the first line. 2.Readwhattheyhavedonepreviouslyandexplainwhatparticularpartoftheirwork you like most. Give all the details about when will the internship take place (i.e. full
  49. 49. 49 / 54 Internships time,5monthstartingFebruary),describeanyparticularexperiencesyouhaveand 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 thelab.EspeciallyiftherearePhDstudentsorothermasterstudentsinthelab,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’tforgettointroduceinyourdiscussionthequestionoftheremuneration.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 startingtheinternship,ifthereissomethingyouwouldliketofollow,askyourPIifit 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 know You 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.
  50. 50. 50 / 54 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 processendofaugust,beginningofseptember.Forthesecondandthirdinternships, youshouldhavefoundalab,typicallyonemonthbeforethestartingdatetoletsome 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- shipscouldbethefirstone,asPIsaresearchingquiteearlyforcandidates(theywant 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. -InterviewsforPhDinternshipsareextremelycompetitive.Thebetteryouknowthe teamandtheproject,thebetterforyou.Ofcourseitispossibletoprepareapresen- tationonaPhDprojectintwoweeks,butitwillsurelybemoredifficultandstressful 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’sstillgood.Butit’struethat“positions”arebeingoccupiedfastandyoumighthave 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
  51. 51. 51 / 54 Internships 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 ! InFrance,labrotationsareregulatedbylaw.Thelaboratoryinwhichyouwillperform yourinternshiphastosignabindingagreementwiththeuniversityyouareregistered to before you can start to work. It is a rigid and slow system since many different actorshavetosignthesamedocumentinfourcopies.Thesedocumentsareavailable onthewebsitesofParisDiderotandParisDescartesuniversitiesandontheMoodle (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 internationalinternshipsandittakesevenlongertogetthesigneddocument,sobe 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
  52. 52. 52 / 54 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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  54. 54. Master AIRE Centre de Recherche Interdisciplinaire 8-10 rue Charles V 75004, Paris.

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