FDV 2015 2106 Program

COLE DOCTORALE
DOCTORAL SCHOOL
2015-2016 Program Handbook
cole Doctorale Frontires du Vivant (FdV)

Frontiers of Life Sciences Doctoral School
FdV PhD
Centre de Recherches Interdisciplinaires
8-10 rue Charles V
75004, Paris.
http://cri-paris.org/doctoral-school-fdv/
Dear FdV PhD Student,

We are happy to welcome you to our PhD program.
This booklet summarizes most of the courses and opportunities offered by our program. Its goal is to guide you through the
year and help you make the most out of it. Together, we will
make sure that your time spent at the Center for Research and
Interdisciplinarity in Paris is exciting and productive.
The FdV PhD Team
Contents
1. About the FdV program
2. FdV Program guidelines
1.1 Life sciences

1.2 Education and discovery
2.1
2.2
2.3
2.4
2.5
2.6
2.7
2.8
2.9
FdV spirit
Admission to the PhD program
Training program
Thesis advisory committee
Criteria for doctoral degree
Duration of the thesis
Post-thesis preparation and follow-up
Signatures and acknowledgments
Website representation and student network
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3. Thesis advisory committee guidelines
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4. Annual Training Report
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5. Reimbursement Procedure
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6. FdV Training Program
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7. Important Contacts
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3.1
3.2
3.3
3.4
3.5
Tutor selection
Thesis Summary Report (TAC Report)
TAC Meeting and Tutors Report
Submission of TAC Reports
TAC Budget
4.1 Online Platform
6.1
6.2
6.3
6.4
7.1
7.2
7.3
7.4
7.5
Required FdV courses and workshops

la carte FdV Courses and Workshops
DIY your PhD curriculum
Student initiatives
FdV PhD Program contact
FdV Support and CRI contacts
Other CRI programs
Paris Descartes University Contacts
Paris Diderot University Contacts
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1. About the FdV program

The Frontires du Vivant (FdV) PhD program, established in 2006, is a joint
program between Paris Descartes and Paris Diderot (Paris Descartes etablissement porteur). It is part of the Programme Bettencourt created and
funded by the Bettencourt-Schueller Foundation to help creative and talented
students develop their PhD in an environment as enriching as those of the
best graduate programs in the world. It is one of the 32 doctoral schools hosted at the Sorbonne Paris Cit University (USPC). The disciplines covered by
the doctoral school are broad and include natural sciences, engineering and
technology, medical and health sciences, and social sciences.
The aim of this interdisciplinary doctoral school is to promote ambitious research projects involving interactions between a broad range of academic
disciplines in the pursuit of understanding living systems and/or education
and discovery. Thus, the FdV graduate school recruits students trained in
various disciplines (e.g. biology, physics, medicine, economy, linguistics)
from around the world.
A number of research aims are associated to the FdV doctoral school due the
interdisciplinary nature of the program. They can be broadly categorized into
two main topics: life sciences and education/discovery.
1.1 Life sciences

Since the creation of the FdV doctoral school in 2006, the aims were focused
on interdisciplinary research involving life sciences. As of August 2015, over
100 PhDs have been granted to FdV fellows studying topics at the frontiers of
life science, and over 100 more are currently in pursuit of their degree.
1.2 Education and discovery

Starting in 2014, the FdV PhD program began hosting projects at the frontiers
of learning and discovery. Research projects related to this frontier involve
learning with games, teaching through research, communication technologies, participatory science, etc.
The FdV guidelines are based on the five-year project (2014-2018) of the
doctoral school approved in 2013 by the AERES, the french evaluation agency for research and higher education.
2.1 FdV spirit

The pedagogical project of FdV is focused on the active participation of the
PhD fellows in their own education at the frontiers of knowledge. The FdV
program fosters an environment of cooperation and excellence in the FdV
program that enables students to develop their potential as young researchers. The program enables labs to host unconventional theses, with respect
to their usual doctoral school, to participate in an interdisciplinary community,
and to take advantage of resources made available by the school through
their fellows.
2.2 Admission to the PhD program

Candidates must present themselves and the PhD project for evaluation by
the International Scientific Council. Fellowships for the doctoral school are
awarded according to the candidates ranking after the recruitment selection
and the available annual financial resources.
Hosting labs are committed to support and facilitate the participation of their
FdV PhD fellows in the school program.
University registration
FdV students must be registered with either Paris Descartes University or
Paris Diderot University for every year of their PhD studies. At the beginning
of each academic year, all students must register. Registration does not automatically renew from one academic year to the next. The administrative
registration deadline is in mis November of each year, but please refer to the
university specific documents for the exact deadlines.
Please note that the PhD diploma is issued by the universities, not by the
doctoral school. Thus it is imperative that students are registered, otherwise
the diploma and student benefits cannot be granted.
Please contact the FdV staff if you have any questions about the university
registration procedures.
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Chapter 2
2. FdV Program guidelines
PhD Funding
All PhD students must have doctoral funding for three years. Since the graduate school is not able to support all the eligible candidates, fellows and their
supervisors are encouraged to apply with the help of the program for funding
available from other institutions.
In most cases, funding is issued to the student through the university. However, it is also possible to have an agreement between the university and any
funding provider such that the students stipend is issued to him/her from the
funding provider directly. In either case, all students must have explicit funding for his/her doctoral studies. Please contact FdV staff for any questions
related to FdV funding.
2.3 Training program

The FdV Bettencourt PhD Program offers an extensive doctoral training program that combines research with a curriculum of advanced courses and
workshops on interdisciplinary research, science-related topics and transversal skills for scientific professions. The interdisciplinary nature of FdV program fellows interests and projects requires a broad set of skills and knowledge. Fellows are required to validate at least 300 hours of academic training
including advanced, interactive training sessions, fellow-led science clubs,
workshops, and conferences before the thesis defense is granted.
At least half of this training should be earned through FdV courses, workshops, and other activities organized by the Center for Research and Interdisciplinary (CRI). The remaining hours may be validated through courses
taken at other institutions in France and abroad, massive open online courses (MOOC), international meetings and summer schools, teaching activities,
etc. upon prior agreement with the FdV staff.
A number of FdV courses are mandatory for each student to complete before
the end of their third year of studies. These courses aim to develop the transversal skills necessary in the research community such as scientific communication, interdisciplinary collaboration, and responsible research practices.
To foster scientific communication and community building in the FdV doctoral school, students are expected to participate in student seminars and
workshops throughout their studies.
Interdisciplinary Fridays
During the first year, students will give a short presentation to a general audience to introduce their project, main issues, and approaches. Because these
presentations are held in front of an audience of student researchers from
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Thematic Workshops
The second year presentation occurs during the thematic workshops, which
group more specialized FdV students, AIV Master students, and participants
of their labs. While the type of presentation may take many forms, e.g. powerpoint/slides, poster, group presentation, demonstration, etc., the aim is for
more advanced and specialized research discussions.
International Conferences
Students must also participate in at least two international workshops/conferences during their thesis to maximize the visibility of their work and develop
contacts for their scientific projects. To this aim the program provides up to
1000 euros per year per fellow to help cover the expenses for attending international workshops and conferences.
Additional funding resources are available for conference travel through Paris Descartes and Paris Diderot universities. Please see the respective university websites for more information about eligibility, application procedure,
award amount, etc.
University Paris Descartes: Bourses doctorales de mobilit de luniversit
http://ecolesdoctorales.parisdescartes.fr/Mobilite-Internationale/Bourses-doctorales-de-mobilite-de-l-universite-BDMU
University Paris Diderot: Mobilit dtudes en doctorat
http://www.univ-paris-diderot.fr/sc/site.php?bc=international&np=mobilitedoctorat&g=m
Annual Training Report

At the end of the academic year, students are expected to submit a training
report where they indicate the courses and training hours accrued during the
year. Please see the Annual Training Report section for details.
2.4 Thesis advisory committee

A Thesis Advisory Committee (TAC) follows the student throughout their PhD.
Its role is to ensure the progress of the research, with respect to the original
aims and in the light of new advances in the field, as well as the general well
being of the fellow. The TAC consists of the PhD supervisor(s) and two senior
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Chapter 2
a variety of backgrounds, this is an effective training for accessible communication. These seminars are intended to promote discussions and scientific exchange among the students and to build the interdisciplinary scientific
community.
scientists (tutors) of complementary expertise to cover the different interdisciplinary facets of the students project. The tutors should work outside of the
supervisors labs and should not be past or present collaborators of the supervisor. The TAC tutors are selected by the student and should be approved
by the PhD supervisor before final approval from the FdV director of studies.
The PhD student meets with the TAC members at least once per year. The
first meeting should take place six months after the start of the PhD. Because
this meeting occurs relatively quickly after the start of the PhD, the purpose
of the first TAC meeting is not necessarily to present results, but to evaluate
the current stage of the research and further develop the plan for the coming
year. The subsequent meetings should take place no more than one year
apart.
Before each meeting, the fellow submits a written progress report to the
members of the TAC. During the meeting, the progress of the PhD work is
discussed and the TAC provides advice and criticism on the proposed research plan for the next year(s). The TAC will also advise the fellow on scientific and career issues and on the choice of conferences and training courses.
The TAC members are expected to complete the tutors report with feedback
for the student on his/her research progress, plan, and training program.
Copies of the students TAC report and tutors report should be submitted to
the doctoral school with the end of the year training report.
Please see the Thesis Advisory Committee Guidelines section for more details.
2.5 Criteria for doctoral degree

The PhD at the FdV program represents a research experience gained in the
hosting lab together with training and experience in science and science-related activities gained through the doctoral school.
Approval to defend the thesis is granted by the doctoral school director. The
director will consider the following: the Thesis Advisory Committee recommendations, scientific achievements, publications or expected publications
resulting from the thesis, and completion of the doctoral school training program including courses, attended conferences, and involvement in the FdV
doctoral program.
The doctoral school does not require a determined number of publications to
authorize the defense. Rather, the defense criteria rely on the quality of the
thesis manuscript, the doctoral training, experience gained during the thesis,
and the capacity to defend within three years.
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One research article written with the lab, not necessarily as lead author, and
not necessarily on the students main subject
One review type article, taking advantage of the work of interdisciplinary synthesis expected by the school
One research article as lead author on the students main subject
The doctorate degree is awarded by the universities (University Paris Descartes or University Paris Diderot), not the doctoral school, after examination
of the candidates work by two reviewers and defense in front of the doctoral
jury.
The jury has the possibility to deliver the doctorate with one of the following grades: a) honorable b) trs honorable, c) trs honorable avec flicitations. The highest grade, trs honorable avec flicitations, is reserved
for candidates with exceptional skills proven by their achievements and the
quality of their thesis defense. This grade can be awarded only if a) there is a
unanimous agreement of the thesis jury members under an anonymous vote
and b) the jury president writes and signs an additional report justifying this
distinction (this report is distinct from the thesis defense report).
2.6 Duration of the thesis

PhD students at the FdV PhD program are expected to finish their PhD in
three years. Extensions are only granted under exceptional circumstances
and need the approval of the Thesis Advisory Committee and the director of
the doctoral school. Extensions will only be considered if funding is available.
Students must submit a fourth year registration request form, available on
the FdV website, to the FdV office. Additional procedures for each of Paris
Descartes and Diderot are available on the FdV website.
2.7 Post-thesis preparation and follow-up

The FdV program will provide training and assistance to help fellows and
alumni to initiate a successful professional career after the thesis.
When publications related to the PhD work are accepted before or even after the defense (if publications were delayed), the FdV school should be informed to maximize the visibility of the fellows achievements. FdV alumni will
be featured on the doctoral schools web site to facilitate contact between
current students and alumni. To keep the strength of the FdV community,
alumni will be invited to various FdV scientific events and are encouraged to
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Chapter 2
However, the doctoral school recommends that the students are involved in
3 publications during their thesis:
participate in and maintain an FdV alumni network.
2.8 Signatures and acknowledgments

Signature regulations of the hosting lab and employer must be respected. In
particular, fellows holding a contrat doctoral fellowship with university funds
must include following affiliations on their publications:
1) Funding university (Paris Descartes or Paris Diderot), Sorbonne Paris
Cit, Paris, France.
2) University where the PhD takes place (if different from the funding university), lab name, unit label (e.g. CNRS UMR, INSERM U), post code, city,
country.
Holders of a contrat doctoral paid from non university funds (case of convention between an external payer organism and the university) only have to
mention in the signature the university where the PhD takes place.
Due to the financial support they receive, FdV fellows are also expected to
rightfully acknowledge, their funding organisms and the Ecole Doctorale
Frontires du Vivant (FdV) Programme Bettencourt.
2.9 Website representation and student network

At the beginning of their PhD, students are asked to sign a photo release form
giving the CRI permission to use photos and/or videos of the themselves on
the CRI website and other advertising venues. Please see the release form
for more details. Students may opt out of the photo release at any time by
submitting a new photo release form to the FdV office indicating that they
do not grant permission for the CRI to publish photos/videos featuring the
student. In this case, the CRI staff will do their best to remove existing photos
and videos from published materials, but cannot guarantee that everything is
removed immediately.
Student website profile

The FdV staff will create a basic academic profile page for each student on
the FdV website. The page will contain the thesis title, abstract, supervisor,
hosting lab, funding source, and photo of the student. This information will
be taken from the original FdV application. Students may update their profile
content at any time by emailing the FdV office with the necessary changes.
CRI Moodle
FdV students may contact other FdV students, alumni, CRI students, and
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Forum for FdV PhD courses and activities: for posts about courses, activities,
thesis defenses, etc.
Forum for non-CRI PhD related information: for posts about anything you
want to share including external courses, seminars, tips, etc.
Forum for post-docs and job information
Forum for general CRI activities: for posts about courses, activities, etc. to be
shared with all CRI members
Scientific ethics and responsible conduct

Ethical behavior is expected during the course of the PhD. This includes originality and reproducibility of the results generated and confidential treatment
of privileged communications.
The financial support by the doctoral school (to attend conferences and
workshops), yearly registration renewal at the university, and authorization
to defend are conditional upon the respect of the present guidelines (e.g.
organization of the yearly TAC meeting, attendance to mandatory courses,
realization of a approximately 100 hours training per year).
For any questions or concerns about these FdV guidelines, please contact
the FdV staff.
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Chapter 2
partners through the CRI Moodle. Students will be given a login to the Moodle at the beginning of their PhD which will give them access to a number of
resources including two forums:
3. Thesis advisory committee guidelines

The Thesis Advisory Committee (TAC) meeting are meant to help the FdV
candidate progress, to plan the project for the forthcoming year, and to promote scientific exchange. They aim to summarize and analyze the research
results obtained thus far, which will provide the basis for discussing and
drawing up a research plan for the coming year. During the meetings the
PhD candidate should give a 30 minute talk followed by a discussion about
the progress of the PhD. The tutors can give advice on measures to be taken
with regard to supervision and/or education and training. They are asked
to evaluate the candidates progress and express recommendations in their
tutors report.
3.1 Tutor selection

The TAC consists of the PhD supervisor(s) and two senior scientists (tutors)
of complementary expertise to cover the different interdisciplinary facets of
the students project. The tutors should work outside of the supervisors labs
and should not be past or present collaborators of the supervisor. The TAC
tutors are selected by the student and should be approved by the PhD supervisor before final approval from the FdV director of studies.
First year FdV students must submit the selection of their TAC committee
members within 1 month of start their PhD. We recommend that you share
these TAC meeting guidelines with your tutors so they can familiarize themselves with the TAC process. Please indicate your selection of your TAC
members using the Tutors Selection Form available on the FdV website.
3.2 Thesis Summary Report (TAC Report)

At least one week before the meeting, the PhD candidates should send a
summary of their research (TAC Report) to the TAC members. The guidelines
for the report content and length are the following:

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For 1st year candidates the summary is intended as an updated thesis

project (~10 pages). It should be structured as a research proposal and
should discuss the existing experimental and theoretical bases of the
subject and preliminary results.
The 2nd year summary should grow to an intermediary summary (~15
pages) including scientific context, the aims, results, conclusions and
perspective on the remaining work to be done.
Building on the previous documents, the 3rd year summary (~30 pages)
aims to provide an outline of the thesis manuscript.
1. What were the most important results since the last meeting (or since
the beginning of the PhD for 1st year candidates), in terms of scientific
achievements and progress in your work?
2. Were there changes in the project since the last meeting (or since the
beginning of the PhD for 1st year candidates)? If so, what was the cause
of the changes and/or delay and what was the response to this?
3. What were the principal difficulties encountered? What measures of actions have been undertaken in response?
In addition, the PhD candidate should also take advantage of the TAC report
to include questions on issues they would like to address during the meeting.
3.3 TAC Meeting and Tutors Report

The PhD candidate is responsible for organizing the TAC meeting with the
tutors and the thesis supervisor(s). External guests can be invited. The first
meeting should occur 6 months after the beginning of the PhD and then every year thereafter. Because the first meeting occurs relatively quickly after
the start of the PhD, its purpose is not necessarily to present results, but to
evaluate the current stage of the research and further develop the plan for
the coming year.
During the meeting the PhD candidate gives an oral presentation (30 minutes) of the research project, during which, specific scientific problems can
be addressed. The candidate is invited to bring to the meeting his/her lab
books, in order to be able to answer questions and get more precise feedback on experimental and theoretical work.
Following the general discussion, the tutors should meet with the student
separately without his/her supervisor(s). Then, the tutors should meet with
the supervisor(s) without the student present. The tutors should then deliberate alone, during which time they will discuss and summarize their views and
formulate their recommendations. The tutors should use the Tutors Report
Form to give the student feedback on the presentation, research progress,
and PhD training. All responses must be typed in English and signed by the
tutors. The Tutors Report Form is available for download on the FdV website.
The comments are then discussed in group the group.
After the TAC meeting, the PhD candidate needs to sign the tutors report and
collect the signatures from the tutors. Handwritten signatures are preferred,
but electronic signatures will be accepted. The students must send the (i) the
thesis summary, and (ii) the TAC meeting report in PDF format to the doctoral
school through the online platform.
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Chapter 3
In order to prepare the discussions at the meeting the document should also
address the following questions:
3.4 Submission of TAC Reports

FdV students are expected to submit their TAC report and tutors report to the
FdV doctoral school. The TAC documents should be uploaded to the Google
Drive folder with the annual training report by the 1st of July. Please see the
section on the annual training report for details on accessing the Google
Drive folder. Additionally, students should periodically visit the FdV website
and check his/her cri-paris.org email for any changes to the submission process.
3.5 TAC Budget

In order to encourage the exchanges between the PhD candidate, the TAC
members and possible guests on the day of the TAC meeting, a budget of up
to 200 is available from the doctoral school for lunch. For reimbursement
the candidate should return the receipt and invoice (with the name of the
participants) to the FdV office. Please see the reimbursement procedures for
more details.
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4. Annual Training Report

FdV students may earn their 300 hours of training in a number of ways including FdV and external courses, workshops, conferences, teaching, CRI
activities, etc. At the end of the academic year, students are expected to
report all of their training hours to the FdV doctoral school through the Annual
Training Report.
Once the report is completed, FdV staff will validate the hours, record overall
progress, and provide feedback on the training.
Each student has a Google drive folder that is shared with the FdV staff. Students can access their folder by logging into Google Drive with their cri-paris.
org email address.
The Google Drive folder should be used to upload the annual report documents which include:

Training Report (Google Spreadsheet document, template already loaded into folder)
Supplementary documentation for validation of external trainings
TAC report
Tutors report
Additional documentation is required for validation of external courses, workshops, conferences, etc. Documentation may include a certificate of completion, attestation letter, registration receipt, etc. Documentation is not necessary for required for FdV courses where attendance was taken and reported
to the FdV staff. Once the training report is completed, the FdV staff will
review the documents and provide feedback to the student.
The training reports should be completed and all accompanying documents
uploaded to Google Drive by the first of July.
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Chapter 4
4.1 Online Platform
5. Reimbursement Procedure
FdV PhD students have an annual budget of 1000 euros for conference travel and accommodations1 and an annual budget of 200 euros for the TAC
meetings. Before using any FdV budget, students must receive approval
from the director of studies, which they can obtain by sending an email to
either director (CC the scientific coordinator) and explain how the budget will
be used and how the purchase is relevant for the training program. Once
approved, students may make the purchases.
After returning from the conference, students may submit their reimbursement documents according to the procedure below.
1. Complete the SCIRE Expense Report with signature from David Tareste
or Antoine Tesniere (note: electronic signatures are acceptable)
2. Attach your original receipts and/or invoices
3. Submit your expense report and receipts to Tien Clabaut: tien.clabaut@
cri-paris.org
The SCIRE Expense Report is available for download on the FdV Website.
It is possible to get a cash advance by SCIRE in the case of travel expenses
(not applicable to hotel expenses or seminar entrance fees). In this case,
we will purchase your ticket but we must use a travel agency, which sometimes requires time and management costs, and may thus increase the price
of your ticket. After obtaining approval, please contact Marlyne Nogbou at
marlyne.nogbou@cri-paris.org to make advanced ticket purchases.
1
Each year, the 1000 euro budget must be approved by the director of studies. The financial support is conditional upon the respect of the FdV guidelines (e.g. organization of the yearly
TAC meeting, attendance of mandatory courses, completion of a ~100 hours training per year).
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6. FdV Training Program

The Frontires du Vivant (FdV) Doctoral School is a vibrant community of
talented students from around the world. The unique program leverages
modern educational pedagogy and cutting-edge technology to help young
researchers develop into well-rounded members of the scientific community.
In total, FdV students must complete 300 hours of training during the three
years of the PhD studies. Half of the training hours must be completed
through FdV approved activities, which include the FdV courses listed in
this program. Other FdV activities include participation in scientific clubs,
the Open Lab, Game Lab, Les Savanturiers, teaching and more.
Included in those 300 hours, are the following required courses/workshops
(129-149 hours):
Hours
84-96
hours
Year 2
30
hours
Year 3
15-23
hours
35
2. Interdisciplinary Fridays Seminars
15-20
3. Oral Communication and Public Speaking, choose one:
14-21
General Public Speaking
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Engaging scientific presentations
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Scientific presentations for a non-scientific audience
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4. Critical Analysis of Research Articles
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5. FdV/AIV Thematic Workshops
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6. Written scientific communication, choose one:
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Scientific writing
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Alternative Written Scientific Communication
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7. Well-being, integrity, and responsibility in research intro session
8. Well-being, integrity, and responsibility in research practical session, choose one:
7-15
Managing scientific collaborations: Integrity, negotiation and

conflict
Best DOC: Well-being, health, and work for the doctorate
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Scientific integrity
Responsibility in research and entrepreneurship
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Chapter 6
Year 1
1. Creating Interdisciplinary Research Projects Workshop
In keeping with the spirit of the FdV program, the required courses are designed to develop the transversal skills necessary for the research world.
While we strongly recommend that all students take the courses above, we
understand that in some cases students have already completed similar trainings or have found alternative means to develop the particular skills. In this
case, students should contact the FdV staff customize their curriculum plan.
The requirements for hours validation is described for each course. In the
case that a student cannot meet the requirements for validation, he/she is
encouraged to talk to the FdV staff and course instructor to make alternative
arrangements.
The remaining training hours (max 50% of training hours) can be earned
through external courses and workshops, international scientific conferences, teaching, etc. Typically journal clubs and research group meetings do
not count towards FdV training hours. Please do not hesitate to contact the
FdV team with questions about validation of training hours.
Students will report all of their training hours in the Annual Training Report
due in July, which will be reviewed and validated by FdV staff.
6.1 Required FdV courses and workshops

Students must register for each course they wish to take, including the required courses, on Google Classroom using their cri-paris.org email address
and the Google Classroom Registration code.
The required courses can be found on the following pages:
Requirement 1 pg 20
Requirement 2 pg 21
Requirement 3 pg 22
Requirement 4 pg 23
Requirement 5 pg 26
Requirement 6 pg 27
Requirement 7 pg 28
Requirement 8 pg 29
Requirement 1: Creating Interdisciplinary Research Projects Workshop

Objective: The CIRP workshop intends to assemble free spirited students
and researchers from broad scientific backgrounds to conceive creative research projects. This workshop provides the primary basis for collegiality and
communication through dialogue and brainstorming on open questions in interdisciplinary research project.
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The specific aims are:

To be able to focus on an important scientific question and to define the
means to approach it from different disciplines.
To be able to zoom out (have a broader view) and zoom in (be precise
and define the key experiments).
To think and express your ideas more clearly.
To gain confidence in your ideas.
To be able to discuss, reject or accept ideas.
To learn to take constructive scientific criticisms.
To learn how to write a research proposal.
To discuss scientific questions thoroughly.
To learn to interact with people from different backgrounds.
Coordinator: AIV and FdV Teams
Contact: sofie.leon@cri-paris.org or jeanette.nguyen@cri-paris.org
Dates: Sunday-Friday, 13/9/2015 - 18/9/2015
Location: CIEP center in Svres
Credits: 35 hours
Validation: Students must attend the full workshop to validate the hours and
meet the FdV requirement
Register on the Moodle
Requirement 2: Interdisciplinary Fridays Seminars

Objective: The Interdisciplinary Friday seminars aim to provide an overview
on a wide scope of interdisciplinary research in life sciences and education.
They are intended to promote discussions and scientific exchange among
the fellows and senior scientists and develop an interdisciplinary scientific
community.
Coordinator: Sofie Leon

Contact: sofie.leon@cri-paris.org
Maximum number of students: All 1st year FdV students
Dates: Fridays 18:00-19:00, see FdV Calendar
Location: Room 1.04 at Charles V until the CRI moves, then TBA
Credits: 15 hours
Validation: Student must attend 80% of the sessions and present their PhD
project during one of the IFs to validate the hours and meet the FdV requirement
Google Classroom Registration Code: o3dav2
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Chapter 6
Each session consists of 2 short talks (~15 minutes) aimed at a general but
scientific audience by first year FdV students introducing their research question and experimental/theoretical strategy followed by a discussion. The student should present the general scientific questions addressed in his/her lab
and then focus on his/her specific research work.
Requirement 3: Critical Analysis of Research Articles

Objective: The CARA course is intended prepare students to become reviews of peer-reviewed journals by developing their abilities to read and critically interpret interdisciplinary research papers.
In this course, students will enhance their critical reading skills to identify the
key scientific questions, underlying hypothesis, background and results of
interdisciplinary papers. Article features, such as title, abstract, figures, quality of writing will be analyzed by considering how they support the scientific
content. Students are also asked to suggest further experimental/modeling
approaches with respect to their conclusions from the paper at stake. All
students are expected to participate in the course by reading the selected
papers before the presentation and contributing their insight and questions
during the presentation.
To ensure that students can read the papers in depth, they will be welcome
to choose an interdisciplinary paper that is related to their area of expertise.
We encourage students to consider selecting papers that have not yet been
peer-reviewed, such as those posted on the arXivs: https://www.library.cornell.edu/arxiv
or the biorXivs: http://biorxiv.org/about-biorxiv. In this way, students can act
as reviews and critically read a paper that has not yet been accepted via the
peer-revision process.
Course format:
Introduction session
2 workshop sessions
4 presentation sessions
Special session with Melissa McCartney of AAAS
The course begins with an introduction session where the instructors will
demonstrate a critical analysis of an interdisciplinary paper. Two workshop
style sessions will focus on specific tips and exercises for reading critically.
During each of the presentations sessions, 4 student pairs will have 1 hour to
present their articles. The class will be separated into two groups, such that 2
presentations are occurring in parallel. The students who are not presenting
may select which group they attend. All students are expected to read the papers such that they can engage in the discussion and analysis of the article.
During one special session, we will have former Science Magazine editor,
Melissa McCartney, discuss different styles of publications, journals and the
process of scientific publication.
Instructors: Saskia Van Der Vies and Anne Schmidt
Contact: s.m.vander.vies@vu.nl and anne.schmidt@pasteur.fr
22
Maximum number of students: 32 (8 students per session, 4 sessions)

Dates: Thursdays, 15:30-18:30 25/2, 3/3, 10/3, 17/3, 24/3, 31/3, 7/4, date of
session with Melissa McCartney TBA
Location: To be announced
Credits: 20 hours (8 x 2.5 hour sessions - 1 introduction session, 4 presentation sessions, 2 workshop sessions, 1 special session)
Validation of training hours is based on course attendance and participation,
students can earn up to 20 hours according to the following rubric:
30% course validation for attendance,
30% course validation for presentation of a research paper
40% course validation for the participation throughout the course
Google Classroom Registration Code: 6svgqvj
Requirement 4: Oral Communication and Public Speaking

Requirement objective: Oral communication and public speaking are essentials for scientists and researchers to master. These courses aim to help students effectively communicate their research in a variety of settings.
To meet this requirement, students may take one of the three following courses:

General Public Speaking - intended for students with lower proficiency in

English* (L3 or low L4)
Engaging Scientific Presentations - intended for students with higher proficiency in English* (L4 or L5)
Scientific Presentations for a non-scientific audience - intended for students with higher proficiency in English* (L4 or L5)
General Public Speaking

Objective: The main objective of the course is to (re)discover the tools for an
effective and adapted oral communication. This 2-day workshop is designed
to help young scientific researchers develop their communication skills, with
the primary focus on presentations before small and large groups.
Working from self-evaluation of their skills and objectives, participants will
receive hands-on training in effective techniques in public speaking in academics, including physical preparation (stage presence, voice, non-verbal
communication, branding), organization (structure, materials), content (convincing, storytelling, etc.), audience involvement, and the particular problems
of presenting in a foreign language. Participants should prepare some their
past and current presentations for activities in day 2.
Pedagogic Objectives
23
Chapter 6
* If students have doubt about their level of proficiency in English, they may
contact Sofie Leon for an assessment exam.
To stimulate interaction
To manage stage fright
To encourage effective listening
To develop an individual presentation style
To use the body language
To create effective support materials
To optimize the preparation
Process
Action!
Experimentations to understand the communication basis
Actors techniques to manage the emotions and the verbal/non verbal
aspect of public speaking
Exercises to develop listening, adaptation and attention
Suggestions to master relationship
Techniques to manage the group dynamics
Theory
Instructor: Ray Horn
Contact: ray.horn@free.fr
Maximum number of students: 15
Dates and time: Thursdays, 5, 12, 19 November 2015, 09:30-17:30
Location: Room 3.05 at Charles V
Credits: 21 hours (3 full days)
Validation: Student must attend all three days of the class to validate the
hours and meet the FdV requirement
Google Classroom Registration Code: nwnt2n
Engaging scientific presentations
Objective: Students will learn to deliver scientific talks that engage their audience and get their message across.
The emphasis of this course will be on having fun while giving scientific talks,
because if the presenter is enjoying him/herself, so will the audience. At the
end of the training session, students will have gained the following skills:
Presenting a clear message
Enjoying the presentation process
Adapting his/her message to the audience and to the allotted time frame
Explaining complex subjects using visual aids
Responding to questions from the audience
During the first day of the workshop, students will be presented with tips and
techniques for delivering an engaging scientific talk, specifically:
Captivating your audience: three principles for making your talk interesting
Planning your presentation
Designing clear and attractive slides
24
Answering questions
How to improve your delivery style
How to seek out opportunities for giving talks
On the second day, students will have the opportunity to deliver a presentation and receive detailed feedback from the course instructor and their peers.
Instructor: David Karlin
Contact: davidgkarlin@gmail.com
Dates: Tuesdays 3, 10 November; 09:30-17:30
Validation: Student must attend both days of the class to validate the hours
and meet the FdV requirement
Google Classroom Registration Code: tj4h37d
Scientific presentations for a non-scientific audience
Objective: Students will learn to deliver scientific presentations to a non-scientific audience while having fun in the process
During the first day of the workshop, students will learn tips and techniques
for effective presentations through a round-table discussion. Specifically, we
will discuss:
Fears and motivations in carrying out public engagement
Captivating a non-specialist audience: three principles for making your
talk interesting
The elements specific to presenting to a non-specialist audience
Planning your presentation
Designing clear and attractive slides
How to improve your delivery style
On the second day, students will have the opportunity to deliver a presentation and receive detailed feedback from the course instructor and their peers.
25
Chapter 6
At the end of the training session, students will have gained the following
skills:
Knowing the most common expectations from non-scientific audiences
Presenting a clear message
Enjoying the presentation process
Adapting the message of the talk to the audience and to the allotted
time-frame
Explaining complex subjects using visual aids
Responding to questions from the audience

Dates: Mondays 2, 9 November; 09:30-17:30
Google Classroom Registration Code: 4487sfm
Requirement 5: FdV/AIV Thematic Workshops

Objective: The thematic workshops give AIV and FdV students an opportunity conceive and organize a workshop to showcase their research and
interests in an interdisciplinary and open setting. The workshops aim to create a setting for discussion and exchange amongst PhD students, Masters
students, and the scientific community at large.
FdV PhD students and AIV M2 students work together to create the thematic
workshops week at the CRI. The students decide on five themes, one for
each club, then register to the thematic club corresponding to the main theme
of their PhD research or M2 internship. The students have the opportunity to
organize each component of the thematic workshop, including format, guest
speakers, scheduling, advertising, etc. A budget is available to the clubs for
invitations of external scientists to participate in the workshop and interact
with the students.
M2 students are expected to present and defend their research internship
before a panel of M2 teachers. The FdV students must also present their PhD
research in the format of their choosing. All presentations should be aimed
for a general, scientific audience and should be connected to the theme of
the day. They should include an introduction to the basic scientific concepts
that define the project, an overview of the latest scientific knowledge in this
area, and a clear description of the scientific questions that the project is
going to address and how these fit into the wider picture of understanding
biological systems.
During the mandatory intro session, details of the workshop organization will
be presented and collectively decided by the group. Students will select the
themes and join the workshop they wish to attend.
Coordinator: 2nd year FdV students and AIV M2 students with help from Sofie Leon and Jeanette Nguyen
Maximum number of students: All 2nd year FdV students and all M2 students
Dates: Intro session on Friday 5/2/2016 15:00-17:00; Workshop 11-15 April
2016, 09:00-17:00
Location: TBA
Credits: 16 hours (2 hour intro session, 1 day of organization/presentation, 1
day of attendance)
26
Validation of training hours is based on course attendance and participation,

students can earn up to 16 hours according to the following rubric:
50% course validation for attending 2 days of the workshop and the intro
session
20% course validation for giving a presentation (of any form - poster,
powerpoint, group presentation, etc.) on your PhD research topic
30% course validation for participation in organizing the thematic workshop in which you present
Google Classroom Registration Code: g28zw7r
Requirement 6: Written scientific communication

Requirement objective: Written communication is essentials for scientists
and researchers to master. These courses aim to help students effectively
communicate their research and scientific findings.
To meet this requirement, students may take one of the following courses:

Scientific writing
Scientific Writing
Objective: The course promotes clarity, fluidity, conciseness, and organization in scientific writing. Students will learn to write fluidly to maintain the
attention of the scientific reader.
Course organization:
Introduction: Write to be read a reader, reviewer, and editor perspective. How to avoid the writing pitfalls that make the memory-bound, attention-bound, time-bound, and knowledge-bound reader stumble.
Module 1: The Why and the How of elements of the standard scientific
paper structure: title, abstract, introduction, body (headings, subheadings,
tables and graphs), conclusion, and references.
Module 2: Elementary principles of composition: reaching clarity, conciseness, organization, precision and fluidity in writing to support the scientific
contribution and be accepted for publication.
Module 3: Identification of writing problems: a walk through process to detect
27
Chapter 6
Based on the book Scientific Writing 2.0: a Reader and Writers guide, the
course promotes clarity, fluidity, conciseness, and organization in scientific
writing. The trainer looks at the scientific writing style through the lens of human factors. To be reader-friendly, course participants write with the reader
scientist in mind (and especially the reviewer and editor). They use checklists
and open-source assessment tools (SWAN, etc) to control the quality of their
figures and of their manuscripts title, abstract, introduction, structure, conclusions and references. They learn how to write fluidly to maintain the attention
of the reader.
fluidity problems at sentence and paragraph level.

The participants bring to the course a published paper they have written or
read and are familiar with. No review, no short letter. The paper should have
informative headings and subheadings. At the end of the course, the participants will know clearly how to improve their writing and their paper.
During an optional half-day session, students can bring a paper they are
working on for one-on-one advice and guidance from the course instructor.
Instructor: Jean-Luc Lebrun
Contact: jllebrun@me.com
Dates: Monday-Tuesday, 23-24 November 9:30-17:30 and optional session
on 25 November 9:30-13:00
Location: Rooms 3.04 and 3.05 in Charles V
Google Classroom Registration Code: gkaasst
For the New Frontiers and FdV students interested in alternative means of
scientific communication, e.g. blogging, websites, social media, you are welcome to enroll in this alternative course. The details of the course are not yet
set and depend upon the number of students enrolled. If you are interested in
taking this course, please register on Google Classroom. You will be notified
of the course details as they are arranged.
Google Classroom Registration Code: ijkxfl5
Requirement 7: Well-being, Integrity, and responsibility in research

Introduction session
Requirement objective: Scientific research often involves complex issues of
maintaining integrity, managing conflict, balancing work and personal life,
dealing with stress, etc. This introduction day presents the four well-being,
integrity, and responsibility in research courses through mini workshops.
During this day-long session, each of the four well-being, integrity, and responsibility in research course instructions will present a 2 hour introduction/
mini workshop related to their main course. All of the main course deal with
similar issues, but in different contexts. Thus, the introduction workshop will
give students a preview to each approach to well-being, integrity, and responsibility in research. After this mandatory day, students will choose which of
the four courses they want to take to meet the total requirement.
28
Coordinator: Sofie Leon with workshops conducted by each of the instructors

Dates: Monday 1 February, 9:00-17:30
Location: TBA
Credits: 8 hours
Validation: Student must attend the entire day to meet the requirement
Google Classroom Registration Code: v8fbey8
Requirement 8: Well-being, integrity, and responsibility in research practical

session
Requirement objective: Scientific research often involves complex issues of
maintaining integrity, managing conflict, balancing work and personal life,
dealing with stress, etc. These courses aim to address some of these common issues in a comfortable, collaborative, and open setting.
To meet this requirement, students must take one of the four following courses:
Scientific integrity
Managing scientific collaborations: Integrity, negotiation and conflict
Content
This interactive session on scientific integrity asks students to find examples
of misconduct in his/her own field that will then be used for discussion in the
class. Before the training, students will be asked to complete the following:
Find an example of misconduct in your field
Read 3 papers that will be sent 3 weeks prior to the training
During the first session, we will prepare interviews to be conducted in your
research labs. The preparation will consist of:
Discussion of values and norms in scientific research
Identify initiatives and proposals that you would like to develop/implement in your research environment (existing or new initiatives welcome)
Collectively design/ adapt a questionnaire
29
Chapter 6
Scientific Integrity
Objectives:
To analyze the practices in your lab, namely: how close/far are research
practices from integrity standards? What is the experience of people
around you with integrity issues? What are the resources (human & technical) available?
Explore the feasibility of implementing initiatives promoting responsible
research in your lab
Value responsible practices in your future career plans
Students will have a couple of weeks between the sessions to conduct 2 interviews in their lab using the questionnaire created in session 1.
During the second session, we will debrief from the interviews and discuss
next steps:
Debrief questionnaire, difficulties encountered, etc.
Discuss examples of concrete initiatives, attitudes and solutions
How to value responsible attitudes in your future career projects, e.g. for
a post-doc application, grant application, etc.
How to enforce responsible attitudes when needed?
Instructor: Livio Riboli-Sasco, Claire Ribrault from Atelier des Jours a Venir
Contact: claire@joursavenir.org and livio@joursavenir.org
Dates: 2 February 9:00-13:00, Day 2 will be 2-3 weeks later, Date TBA
Location: TBA
Credits: 8 hours (2x4 hour sessions)
Validation: Student must attend both half days of the class to validate the
hours and meet the FdV requirement
Google Classroom Registration Code: xhhjabd
Managing scientific collaborations: Integrity, negotiation and conflict
Objectives: Students in the course will learn to manage scientific collaborations, and will specifically learn techniques for negotiations, conflict management, and maintaining their integrity in the context of research collaborations.
The US Office of Research Integrity wrote about scientific collaborations:
we are struck by how many disputes could have been avoided if only the
collaborators had taken a few precautionary steps at the outset. This training session, which includes numerous practical applications, will ensure that
students acquire the right reflexes to manage their scientific collaborations.
The course will address negotiation, conflict management, and integrity in
depth. If a researcher knows how to manage conflicts then he/she will often
avoid them. At the end of the training session, students will have gained the
following skills:
Knowing your personal rights and duties in relation to the collaboration
process
Communicating assertively
Negotiating with collaborations
Managing and solving conflicts
Balancing good research conduct with personal morals
The course will start with a discussion of how and why collaborations fail
and will continue to construct best practice to create successful exchange.
Through case studies and specific instances brought by course participants
students will explore issues related to collaborations, negotiation, and conflict
30
management. Specifically, the course will cover:

Introduction to scientific collaboration: why, how, with whom? The key
principles for ensuring harmonious collaboration Identifying and approaching potential collaborators
Creating a collaboration agreement a highly advisable practice.
Managing collaborations
Assertiveness and negotiation principles and practice
Conflict management including practical applications
Discussion and analysis of issues encountered by trainees
Dates: Tuesday, 2 February 2016; 09:00-17:00
Location: TBA
Credits: 7 hours (1 full day)
Validation: Student must attend the entire day to validate the hours and meet
the FdV requirement
Google Classroom Registration Code: xgxgz
Objective: The Best DOC workshops offer students a space to discuss the
challenging and stressful aspects of the PhD and to provide support to their
peers who are also facing similar issues. Students will gain more control over
their negative emotions and improve their resilience in the PhD program.
It is perfectly normal to face obstacles during the doctoral journey and there
seems to be an increasing awareness among academics of the need for
a specific support during this long adventure. Various institutional initiatives
flourish around the world and intervention programs at schools and universities have shown their efficiency. The SPARK Resilience program, which aims
to help people gain more control over their negative emotions and improve
their resilience skills, has been adapted to address the specific needs of doctoral students in this series of workshops.
During the small group discussion sessions students will collaborate to improve engagement at work, self-motivation, personal growth and well-being;
as well as develop techniques to reduce anxiety, unpleasant/negative emotions and depression.
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Chapter 6
Doing a PhD is a stimulating, but also a challenging and stressful experience, as pointed out in the growing body of literature on doctoral education.
Many stress factors affect PhD students: elaboration of a research project,
integration in a research lab and into various networks, relationships with
the supervisor(s) and with peers, growing competition, quest for funding, the
doctoral writing, solitude, lack of self-confidence, precariousness, uncertain
future, etc.
Instructor: Pascale Haag

Contact: pascale.haag@gmail.com
Dates: Fridays 11/3, 18/3, 25/3, 1/4, 8/4 09:30-12:30
Location: TBA
Validation: Because the course is a small group setting, commitment from all
participants is critical. Thus, we require that students commit to attending all
5 sessions. In emergency situations, students may miss up to one session
and still have the course validated with approval from the course instructor.
Google Classroom Registration Code: qfhxx0
Objective: This course is intended for those students who are interested in
entrepreneurial endeavors as part of their research careers. Students will
gain tools necessary for ethical practices in entrepreneurial work.
This course will feature a number of short modules with external participants
to discuss ethical behavior in research and entrepreneurship. The modules
will cover the following:

Social entrepreneurship and link between research and entrepreneurship

Deepening the concept of Frugal Innovation and Bottom of the Pyramid
markets
Intellectual Property issues and innovative IP management for collaborative work
Apply these concepts to the actual research work of the students
Round-table discussion with invited guests based on students interests
Instructor: Melanie Marcel

Contact: melanie.marcel@soscience.org
Date: Tuesday, 2 February 2016; 09:00-17:00
Location: TBA
Credits: 7 hours (1 full day)
Validation: Student must attend the entire day to validate the hours and meet
the FdV requirement
Google Classroom Registration Code: z6n670i
6.2 la carte FdV Courses and Workshops

FdV offers a number of technical, teaching and transversal skills courses.
Many of the following courses require a minimum number of registered students to be held. Registration numbers will be evaluated based on the number of students enrolled on Google Classroom. If the minimum number of
32
students is not met, the course may be canceled.

The different types of courses begin on the following pages:
Technical courses pg 33
Teaching courses pg 42
Transversal courses pg 45
Technical courses
Biological Physics of the Developing Embryo
Investigators with expertise in physics and computational biology collaborate with developmental biologists to understand how forces shape animal
form (Purnel BA, Science 2012). Taking the book Biological physics of the
developing embryo of Gabor Forgacs and Stuart A Newman as a guideline,
we will discuss several physical aspects that underlie and guide a variety of
processes that are involved in early embryonic development.
Instructor: Annemiek Cornelissen

Contact: annemiek.cornelissen@univ-paris-diderot.fr
Dates: Mondays 19/10/15, 16/11/15, 14/12/15, 11/1/16, 8/2/16, 7/3/15,
11/4/16, 9/5/16, 6/6/16, 4/7/15; 09:30-12:30
Location: Room 3.05 of Charles V until the CRI moves, then TBA
Validation:
Less than 50% attendance = 0 hours validated
50%-80% attendance = number of hours validated equal the number of
hours attended
80% or more = 100% of hours validated
Google Classroom Registration Code: fs6i59e
Life Science of Naruto?!
Objective: Apart from having the pleasure to (re)discover Naruto, or to discover at least what everybody around you know and you dont(!), the aim of
this module is to use this Manga series to discuss:
The deep significance that we can find in the story and behaviors shown.
This part is mostly about cognitive/neurosciences and psychology. It
shows how we can describe the functioning of our brain, from very clear
and detailed examples.
The analogies that can be drawn from some aspect of Narutos world, or
how they can be related to common biological theories. The idea is to
33
Chapter 6
In the first session, we will select the aspects on which we would like to focus.
In subsequent sessions we will deepen the course by discussing recent research papers and/or inviting experts in the field. The course meets one time
per month for the duration of the academic year, thus giving students time to
read and reflect on the topics and find connections to his/her own research
in between sessions.
reveal them and then to discuss and challenge them.

Each session will begin with a viewing of an episode or parts of episodes of
Naruto and will continue with a discussion around the theme of the day. The
discussion can then go on about the meaning of analogies, their significance
and importance, usefulness. Some possible themes include:

Naruto and cognitive sciences: perception and interpretation (with illusions and their mastering), communication and language (and what is
actually communicated) and an original (involuntary?) representation of
the unconscious brain.
Naruto and psychology: individual freedom, predetermination, social interactions, resilience
Naruto and Biology: notion of life (vital fluid? what is alive? dead?) the
individual, the notion of species, trans-species and bifurcating ones and
an (involuntary) and original representation of DNA encoding
Instructor: Stephane Douady

Contact: stephane.douady@univ-paris-diderot.fr
Dates: Tuesdays 13/10, 20/10, 27/10, 3/11, 10/11, 17/11; 18:00-21:00
Location: Room 3.05 of Charles V
Validation:
hours attended
Google Classroom Registration Code: ugbeyi
Stat Yourself
Learn a bit more about statistics and how to apply techniques to your specific research project. The course is informal, just sign up if you would like to
broaden your knowledge in statistics. The topics covered and will be based
on students interest.
Instructor: Stephane Douady
Contact: stephane.douady@univ-paris-diderot.fr
Dates: Tuesdays 18/11, 25/11, 2/12, 9/12; 15:00-18:00
Location: Room 3.05 of Charles V
Validation:
hours attended
Google Classroom Registration Code: n57ncm2
34
One Week Immersion into Python Programming for Scientist

Objective: The aim of the course is to provide an intensive introduction to
Computer Programming using the Python programming language.
This course will cover basics to advanced programming skills that youll learn
almost exclusively solving problems and exercises of a daily-based progressive difficulty. While this course is both adequate for people without any prior
experience in programming, and to those having already programmed but
who are willing to get better.
During the weekday sessions students will be presented with numerous exercises with a level of difficulty spanning from very easy to very hard. The
idea is that anyone can start doing the exercises and struggle at the point of
difficulty that will make him/her improve his/her understanding and abilities
to code. During the weekend sessions, students will team up to realize a
project. They will be given a choice between several projects involving scientific computing, web, network, etc. This will be an opportunity to realize a full
program and to discover libraries (i.e.. existing code) adapted to their area
of expertise.
Instructor: Antoine Angot
Dates: Monday-Friday 21-25/9 mentors available 9:00-22:00 daily
Location: Charles V, 3rd floor
Validation: Up to 35 hours based on approval from instructors
Enroll here: http://goo.gl/forms/PR5Ap9N9x3
Managing data and workflows The electronic equivalent to the lab notebook
How computers handle data
Keeping track of data that changes over time
Making computational analyses reproducible
Writing simple programs for data analysis and visualization
Collaborating in a team or with the whole world
Tracking changes who did what, when, and why?
Collaborating on the Web
Electronic publishing
Some of the tools we explore include github, automator, mendeley, etc.
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Chapter 6
Introduction to computer-aided research

Most of todays research requires the use of computers, for tasks such as
data capture, data analysis, visualization, numerical evaluation of theoretical
models, team collaboration, and publication. This course provides an introduction to the techniques and tools that permit to handle these tasks reliably
and efficiently. The topics covered in the course are the following:
Instructor: Konrad Hinsen

Contact: research@khinsen.fastmail.net
Dates: Thursdays 10:00-13:00, 14/1, 21/1, 28/1, 4/2
Location: TBA
Credits: 12 hours - 4 sessions of 3 hours each
Validation: 12 hours
hours attended
Google Classroom Registration Code: y4ikff
Whole cell modeling
Objective: In this course students will learn about and implement a physiological model of a cell then propose their own improvements and additions
inspired by their research interests.
Description:
A large amount of work has been devoted to the mathematical and computational modeling of specific cellular processes. As accurate as these models
may be, their isolation from the physiological cellular context hampers the
study of the role they can play in global cellular behaviors. A whole cell model
is an aggregate of mathematical representations of cellular subprocesses
(e.g. translation, protein maturation, etc.) [see an example of a whole cell
model]. Of course, such submodels need to be validated against experimental data. Eventually, we expect the aggregate model to explain high level
behaviors of a cell like the growth rate. During this hands-on workshop, such
a model will be realized.
Format:
Participants will be divided into several groups. In part 1 of the course, the
groups will implement a base model of a cell then they will propose extensions to the model based on their research interests and expertise. This will
be the occasion to ask questions, draw and test hypotheses about very exciting emergent phenomena at both the cellular and population scales, in a
research-like fashion. In part 2 of the course, one week later, students will
complete their implementations and present their extensions to each other.
The models will be written and simulated in MATLAB.
Instructor: Vincent Danos and Guillaume Terradot
Contact: vincent.danos@gmail.com
Dates: Part 1: 29/2/16-2/3/16 and Part 2: 7/3/16-8/3/16; 9:30-17:30
Location: TBA
36
Validation: Up to 35 hours based on approval from instructors

Google Classroom Registration Code: 38e910
Introduction to multi-algorithm whole-cell modeling
Objective: The objective of this course is to provide an overview of multi-algorithm whole-cell modeling, discuss open questions in the field, and give
students the tools to implement such models.
Description: Whole-cell models are computational models which describe
how cellular phenotypes arise from genotype by accounting for every gene
function and predicting the dynamics of every molecular species over the entire cell cycle. Whole-cell models can be constructed by combining multiple
sub-models of individual pathways (e.g. transcription, translation, metabolism), each described using different mathematics (e.g. differential equations,
Boolean rules, flux balance analysis) and trained using different experimental
data (RNA-seq, mass-spectrometry, kinetic assays), into a single model, enabling modelers to take advantage of existing, heterogeneous pathway models and experimental data. Whole-cell models have the potential to enable
engineers to rationally design microorganisms and enable clinicians to tailor
medical therapy to individual patients.
This course will introduce students to whole-cell modeling including the theory of multi-algorithm modeling, how to construct whole-cell models, and the
existing software tools for whole-cell modeling. In addition, the course will
outline the major open challenges in whole-cell modeling. The course will
focus on concepts and tools which are important to whole-cell modeling.
An introductory lecture will be given on the Friday prior to the course during
the Interdisciplinary Friday seminar time.
Recommended Prerequisites:
Knowledge of systems biology
Knowledge of dynamical modeling including ordinary differential equations,
logical modeling, and flux balance analysis
Knowledge of MATLAB
Instructor: Jonathan Karr of Icahn School of Medicine at Mount Sinai
Contact: karr@mssm.edu
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Chapter 6
Format:
The course will begin with interactive lectures which will introduce students
to the main concepts in whole-cell modeling. Next, the course will have two
hands-on tutorials on multi-algorithm modeling and how to use a published
whole-cell model of Mycoplasma genitalium. In the first tutorial students will
construct a model composed of sub-models of metabolism, transcription,
translation, and RNA degradation. The course will conclude with an open
discussion on the state and future of whole-cell modeling.
Dates: Intro lecture on Friday 25/4 18:00-19:00 and the 2 day workshop on
29-30 April 09:30-17:30
Location: TBA
Validation: Up to 14 hours based on approval from instructor
Google Classroom Registration Code: jk7odxz
Chemical equilibrium and kinetics inside cells
Objective: This course will be a guide through the different main types of
chemical reactions inside cells, the existing models to describe them and the
available techniques to measure them.
The course will cover the following topics through discussions
Types of chemical reactions within cells
Protein folding and conformational changes
Enzymatic reactions
Dimerizations and oligomerizations
Partitioning between different cellular compartments
Macromolecular assemblies
Revision of thermodynamics and chemical kinetics
Differences between chemical reactions in the test tube and inside the
cell. Existence of background interactions.
Molecular crowding
Confinement
Adsorption
Models to describe them
Introduction to some of the existing methods to study chemical reactions
inside cells. Worked examples for each case
Atomic force microscopy
Single molecule tracking
Super-resolution microscopy
Coherent anti-stokes Raman Spectroscopy Microscopy
Optical tweezers
Magnetic tweezers
Optogenetics and magnetogenetics
Students should have an undergraduate level knowledge of thermodynamics, chemical kinetics and quantitative analysis (e.g.. Physical chemistry, a
molecular approach Donald McQuarrie)
Instructor: Amanda Remorino
Contact: amanda.remorino@curie.fr
Dates: Thursdays 16:00-20:00 October 15, 22, 29
Location: Room 3.05 in Charles V
Credits: 12 hours - 3 sessions of 4 hours each
38

hours attended
Google Classroom Registration Code: p4v4a3
Chitchatting cells, lets hear their stories
Objective: The main goal of this course is to give an overview of the role of
local cellular communication in different biological systems ranging from quorum sensing in bacteria to the communication during human brain activity and
immune response. This will be particularly explored by the students during
their research project, which may be focused on their own biological model
(if applicable) or any other topic of interest related to cellular communication.
Description: Global connectivity (phone, internet, social networks, etc.) plays
a fundamental role in our daily living. However, do you know how your cells
communicate with each other? This course we will focus on the different
mechanisms that allow local communication between cells and might impact
the cellular coordination in health and disease.
Format: During the introductory class several mechanisms of cellular communication will be shortly reviewed. After the introduction, the students will
select a mechanism to (1) present a research paper on and (2) develop a research project around. Each subsequent course session will focus on a particular mechanism of cellular communication. The instructor will give a short
but in-depth explanation of that particular mechanisms. Next the students will
be guided to investigate the new discoveries in the field and/or the possible
role of cell communication in their cellular model (if applicable). Finally the
paper about the corresponding topic will be presented by the student(s) who
selected the mechanism. During the final session of the course the students
will present an innovative project about the chosen mechanism.
Students in the course should have some basic prerequisite knowledge of
cell biology.
Instructor: Pablo SAEZ
Contact: pjsaez@gmail.com
39
Chapter 6
The students will review some examples of cellular communication including:

Contact-dependent cellular communication: cytoplasmic bridges (nanotubes), membrane receptors, gap junctions.
Contact-independent cellular communication: exosomes, membrane
channels.
Human cellular communication in health and disease.
In particular, we will investigate two main questions for each mechanism:
1) which type of messages are delivered, and 2) what happens when the
communication is disrupted.
Dates: Tuesdays 12/1/16, 19/1/16, 26/1/16, 2/2/16, 9/2/16, 16/2/16; 17:0019:00

Location: TBA
Credits: 6 sessions of 2 hours
hours attended
Google Classroom Registration Code: j2nasqu
Toy Models and Serious Games
Humanity is facing new challenges in a more complex and open world. New
technologies, new constraints on resources, and, therefore, new sources
of conflicts emerge. Conversely, new computational schemes for collective
organization and action and potential new power structures might take on
these challenges in a way traditional ones cannot. To this effect, this class
will introduce a set of serious games and topical toy models. Through the
understanding and manipulation of these games and models, student players will better apprehend multi-faceted, complex, collective and adversarial
dynamics typical of decision making.
In this class, students will
Get familiar with (some) computational bricks for representing and reasoning about complex situations
Acquire ability to utilize modeling/representational gadgets while understand various levels of technical knowledge - mastery vs delegation
Understand the tradeoffs of modeling
Learn to think about model applicability and exercise critical thinking in
relation to models
Learn how to organize decision making (liquid democracy, participative
democracy, political debate) and how to use models to this effect
Appreciate ethical implications of model based decisions
This project-based course will review a number of diverse models including
those representing:
Stylized economy-energy-climate model
War, space, and the evolution of Old World complex societies
Opinion formation and fission into multiple communities
Mood modeling and prediction of depression onset
Basic social models: segregation
Microbial growth
Cracking and fragmentation
Plant growth
Urban growth
40
Instructors: Amodsen Chotia, Vincent Danos, Sofie Leon

Contact: vincent.danos@gmail.com, sofie.leon@cri-paris.org
Dates: Spring 2016, exact dates TBA
Location: TBA
Credits: 16 hours (8 sessions of 2 hours each)
Validation is based on course attendance and participation. Students can
earn up to 16 hours based on the recommendation of the instructors.
Google Classroom Registration Code: 5mr6rf
A sustainable synthetic world
Objective: To explore the extent to which the rapidly evolving synthetic biology technology platform is capable of making a robust contribution to meeting some of our greatest global challenges. Some of these include how to
sustainably deliver food, energy, water, and materials to a human population
racing towards 10 billion people.
Format: This course will meet once a week for 2 hours over ten weeks (20
hours total). All students will join a case study project team with the topics for
each team to be selected by the students. The final meeting will be devoted
to presentations by each of the case study teams. This course is open to
students from all backgrounds.
Resources: For students with a limited knowledge of the synthetic biology
technology platform please consider the following two books and website as
useful resources:
George Church and Ed Regis; REGENESIS: How synthetic biology will
reinvent nature and ourselves (2012) [note: buy the latest paperback
edition with the orange cover and a picture of a wooly mammoth]
Robert H. Carlson; BIOLOGY IS TECHNOLOGY: The Promise, Peril,
and New Business of Engineering Life (2011)
A good website to follow commercial developments in Synbio is: synbio41
Chapter 6
Description: Synthetic biology (Synbio) holds the promise to make significant

improvements in overall resource productivity in a range of key sectors from
food to healthcare and energy. This is true for several reasons including: (1)
the rapidly falling costs of sequencing and synthesizing DNA; (2) synthetic
biology can leverage almost all of the ongoing improvements in IT; (3) DNA is
a more robust information platform than binary computer code with billions of
existing applications; and (4) DNA is the only software than makes hardware.
The potential of Synbio to serve as a new technology and growth platform
depends on a range of factors including, technical, economic/commercial,
political, social/ethical, and cultural factors. There is no guarantee that capital markets will invest in those Synbio applications with the greatest potential
to address our sustainability challenges. We already have companies using
Synbio to make synthetic vanilla, milk proteins, and solar fuels. Do these and
other emerging applications have the potential to make a difference to our
exponential demand for, and consumption of, key resources?
beta.com
Instructor: Michael Molitor
Contact: mmolitor@carbonshift.com
Dates: Thursdays 9:30-11:30 1/10, 15/10, 22/10, 29/10, 12/11, 19/11, 26/11,
3/12, 10/12, 17/12
Location: Room 1.04 in Charles V
Credits: 20 hours (10 sessions of 2 hours each)
Validation is based on course attendance and participation. Students can
earn up to 20 hours according to the following rubric:
25% course validation for attendance,
25% course validation for your case study team presentation,
50% course validation for the final research paper
Google Classroom Registration Code: lnyc0ws
Teaching courses
Games to teach and do research
Objective: The aim of this course is to first assess the potential and the limitations of using games to do research and teach, and secondly for participants
to gamify their PhD projects.
Recently, a great number of scientific projects were developed around massive online games (Foldit, Galaxy zoo, Picbreeder, Phylo). Also, it is well recognized that learning can be achieved through playing games. In this course,
we will review some example related to:
1) the use of games to perform a given research subject,
2) scientific research which can be done with games,
3) games to teach a oriented concept, and
4) knowledge one can get from games.
The objective is to assess the potential and the limitations of using games
to teach and do research. In particular, we will discuss normal games to
emphasize the key rules of a successful game play. Eventually we will see
how to gamify your PhD as a concrete and practical example of how to turn
a scientific project into a game.
Instructors: Amodsen Chotia and Raphael Goujet
Contact: amodsen@cri-paris.org and raphael.goujet@cri-paris.org>
Dates: Tuesdays Day 1: 26/4/16 10:00-12:00, Day 2: 3/5/16 10:00-12:00,
Day 3: 10/5/2016 10:00-14:00
Location: TBA
Credits: 8 hours (three sessions: 2h + 2h + 4h)
Validation: 8 hours
42
hours attended
Google Classroom Registration Code: pf30e0p
Introduction to mentoring bachelor students: Reproduce and enhance an experiment of
your PhD project
Objective: This course gives PhD students the opportunity to mentor undergraduate students through a project-based research project. PhD students
will test the reproducibility of their research and explore research directions
that may not have been possible without the team of students working on
their project.
This course offers you the opportunity to experience project-based mentoring
with students in the second year of bachelor studies in the Fronteres du Vivant program. L2 students will work in groups of 3-5 to (1) replicate an experiment proposed by a PhD student researcher; then (2) design and perform
an additional experiment to enhance the previous one. The PhD students will
also be mentored through the project-based teaching process with 3 training
sessions.
The PhD students will see a number of outcomes from this training:
Gain experience in mentoring students in a small group setting
Have one of your experiments reproduced
Have a pilot experiment performed by students: the results of which can
inform future development of similar experiments in your PhD project
Connect your research to your teaching practice
Develop a teaching philosophy that supports autonomous learning of
students
Share different dimensions of the research practice: research methodology, social dimensions, institutional aspects, etc.
Analyze your own teaching practice, with respect to defined pedagogical
objectives
Explore how project-based teaching approach can nurture more classical teaching approaches
No prior teaching experience is required.
Instructors: Livio Riboli-Sasco, Claire Ribrault from Atelier des Jours a Venir
43
Chapter 6
The role of the PhD student will be to

Propose a simple experiment that could be replicated by the L2 students
in 20h, in the lab in Cochin, or outside the lab (cognitive studies, ecology...)
Meet 3-5 times with the students (10h total) to guide them and discuss
results as they replicate the first experiment and design the additional
experiment. The bachelor students will also be guided by other teachers.
Minimum participants: 6
Maximum participants: 10
Dates: April-May 2016: Intro session in April; Mid training session in May;
Final session in May
Location: Training locations TBA, mentoring sessions to be held at the CRI
Lab at Cochin or outside the lab, depending on the type of research project
Credits: 13 hours (3 hours of training sessions + 10 hours of mentoring bachelor students)
Validation: Up to 13 hours validated based on recommendation of instructors
Google Classroom Registration Code: o4xp61r
Advanced mentoring of L3 bachelor students: Lead students through pilot experiments
of your PhD project
Objective: This course gives PhD students the opportunity to mentor undergraduate students through a long-term research project. PhD students
can explore research directions that may not have been possible without the
team of students working on their project.
This course offers you the opportunity to experience project-based mentoring
with students in the third year of bachelor studies in the Fronteres du Vivant
program. The L3 students will work in groups of 3-5 to perform a short preliminary research project, aiming to analyse the relevance and feasibility of a
medium-term research project (~6 months), such as the one they would perform in a masters internship. The PhD students will also be mentored through
the project-based teaching process with 3 training sessions.
The role of the PhD student will be to
Propose a project related to your PhD, that you expect to take about 6
months. The project can be:
One that you plan to do later in your PhD
One that you consider relevant to offer for a 6-month internship.
Guide the L3 bachelor students as they design and perform a pilot or a
series of pilot experiments (about 20-30h in total). While the L3 students
will not continue the project after the course, their preliminary work will
inform future development of this experiment in PhD project
Meet the students regularly to guide them in the project (approximately
4 times). The bachelor students will also be guided by other teachers.
Involve the L3 students in presenting their pilot experiments in one of
your lab meetings
The PhD students will see a number of outcomes from this training:
Gain experience in mentoring students in a small group setting
Have a pilot experiment performed by students: the results of which can
inform future development for your PhD project
Connect your research to your teaching practice
Develop a teaching philosophy that supports autonomous learning of
students
44
Share different dimensions of the research practice: research methodology, social dimensions, institutional aspects, etc.
Analyze your own teaching practice, with respect to defined pedagogical
objectives
Explore how project-based teaching approach can nurture more classical teaching approaches
No prior teaching experience is required. The L3 students will perform the

experiments either (i) in your lab, with a convention daccueil for a total of
about 5 non continuous days in the lab, or (ii) as field experiments (e.g. cognitive experiments, ecology...)
Participants: 3-4
Dates: April-June 2016: Intro session in April; Mid training session in May;
Final session in May
Location: Training locations TBA, Mentoring locations will either be in your
lab or outside the lab, depending on the type of research project
Credits: 25-45 hours (5 hours of training sessions + 20-40 hours of mentoring
bachelor students)
Validation: 25-45 hours validated based on recommendation of instructors
Google Classroom Registration Code: 4ctzqic
Transversal courses
Scientists often use scientific or philosophical notions that have different

meanings, and a rich and complex history. Some examples: information, entropy, epigenetics, complexity, reductionism, law, contingency. We will work
together to characterize these different meanings, and look for what is at
stake behind the use (or non-use) of these notions. A particular attention will
be paid to notions used differently in different scientific disciplines.
Goals
The first step will be to establish together a list of about twenty notions.
Each session will be devoted to the study of one of these notions. It will
be prepared by four students who will describe the main meanings and
uses of these notions
I will complement by adding some historical information on the introduction of these notions, and the different ways there were successively
used
A general discussion will help us to go further in their understanding.
45
Chapter 6
Important and Ambiguous Notions in (Life) Sciences

Objectives: In this course, the students and instructor will work together to
characterize and discuss scientific or philosophical notions that have different
meanings to different people.
Instructor: Michel Morange

Contact: michel.morange23@orange.fr
Dates: Wednesdays 18:00-19:30; 21/10, 4/11, 18/11, 2/12, 16/12, 13/1, 27/1,
10/2, 24/2, 9/3, 23/3, 6/4, 20/4, 4/5
Location: Room 3.05 of Charles V until the CRI moves, then TBA
Validation:
hours attended
Google Classroom Registration Code: 3urgs7
Effective Reading in English
Objective: This course aims to improve efficiency in technical reading in English for non-native speakers
This workshop is designed to help non-native speaking students gain efficiency and speed in reading English for their academic work. While not a
foreign-language course, the workshop will examine certain features of the
language and highlight techniques of speed reading, as well as offering a
look at attendant study skills such as text management and note-taking.
Instructor: Ray Horn
Contact: ray.horn@free.fr
Dates: Late November/Early December TBA
Location: TBA
Validation: Attendance of both days of the course is necessary for validation
Google Classroom Registration Code: reba9u
Typesetting for Scientists
Objective: During this hands-on workshop students will learn how to use LyX,
an easy-to-use typesetting environment that uses the power of LATEX to
produce beautiful, professional documents.
LyX is a document processor that uses LaTeX through an easy-to-use graphical user interface. It is an extremely useful tool for creating professional
formatted documents in LaTeX (journal papers, TAC reports, PhD theses,
etc.) without the need to code in the LaTeX language. By using a typesetting
framework, the focus of your scientific writing is on the content itself rather
than on formatting.
Students will learn to use the software through hand-on exercises led by
the instructor. In the first two sessions we will cover the basic necessities for
46
generating LaTeX documents with LyX, namely:

Basic document settings
Basic type setting
Lists
Document sections
Table of contents and bibliography
Floats (tables and figures)
Labels and referencing
Math and equations
LaTeX preamble and custom code
Importing class and layout files
Exporting to and compiling LaTeX
At the end of the workshop, students may focus on aspects that they would
like to explore in more depth, e.g. mathtype and equations, custom code,
journal-specific class files, etc. Students are encouraged to bring their on
their own document on the second day, e.g. TAC report or journal paper, such
that they have a tangible output from the workshop.
Instructor: Sofie Leon
Dates: 18/2, 19/2 9:00-13:00
Location: TBA
Validation:
hours attended
Google Classroom Registration Code: dbbmi1l
Students will explore the art of conveying a message through a figure and will
create figure(s) for a document they are currently working on, e.g. TAC report
or journal paper, such that they have a tangible output from the workshop.
Students are encouraged to bring their own data to work with it during the
course. Roughly, the course will be outlined as follows:

Introduction: Role of figures in presentations and publications

Introduction to the different types of figures (plots, images, cartoons,
covers, movies) and the messages each of them convey
Build awareness on their relevance and impact
Differences between figures for presentations, publications and posters
47
Chapter 6
Figures for Presentations and Publications

Objective: During this hands-on workshop students will create and/or improve figures to communicate their scientific research for different settings.
Worked examples: assessment of the difference in impact between

articles and presentations with good and bad figures.
Optimization of each type of figure
Plots: types of plots and their purposes (scatter, contour, histograms
etc), axes, labels, legends, condensation of multiple datasets into
one single plot, error bars
Images: types of images (microscopy, protein structures, photos, etc)
resolution, quality, colors.
Cartoons: how to condense a concept in a sketch
Worked examples: comparison of examples from literature
Differences between figures for publications and presentations
Identification of the needs in each case (fast and concise vs. detailed
and extremely rigorous)
Publications: captions, figure guidelines for different journals (size, colors), graphical abstracts, covers
Presentations: how to highlight the relevant aspects of a figure to convey the message quickly, how to guide the audience through the figure
Worked examples: exercises with data provided by the students
Figure finishing
General aesthetics (contrast, color choice, readability)
Achieving a professional look
Different file formats
Instructor: Amanda Remorino
Contact: amanda.remorino@curie.fr
Dates: 18/2, 19/2 14:00-18:00
Location: TBA
Validation:
hours attended
Google Classroom Registration Code: agckpc
Extended scientific literacy
Scientific research practice involves various literacy skills that constitute an
essential part of the research process. Mastering a diversity of expression
tools (e.g. blogs, creative data visualization, graphical abstracts) supports a
responsible practice of research, and in particular it allows transparent dialogue within research communities and society.
This training moves beyond standardized formats of scientific articles and
conference presentations, and leads participants to develop lesser-known
literacy tools specific for their research project. During both individual and
group work, students will develop new forms for expressing and representing
the different facets of their research. They will explore how these different
48
modes of expression contribute to their ongoing research. Students can expect to produce at least one form of expression useful for the development
of their project (e.g. graphical abstracts, data representation, audio file of a
radio style interview, clarification of subtle aspects of their research, sharing
research with citizens).
In addition to developing new material, students will participate in interactive
session to address how their own interpretation processes can be influenced
by their individual subjectivity as well as by implicit rules of the scientific community. Thus, students are expected to be present and actively participate
during the entire course. Assessment will be based on the production of a
new form of expression and on the contribution to other participants work.
Logistics:
Participants leave Paris on Sunday night and return on Wednesday evening
All transportation, food, and accommodation arrangements are included
at no cost to FdV students
Participants: 7-12
Dates: June 2016
Location: Bidart, basque coast (64)
Credits: 21 hours (18 hours of courses and mentoring and 3 hours of personal work over 3 days)
Validation: 21 hours validated based on recommendation of instructors
Google Classroom Registration Code: uqgmaf
Researchers have numerous technical skills, but also other transferable

skills of which many people, including the researcher him/herself, are probably not aware. Such skills may include working in a multicultural environment,
dealing with failure, communicating efficiently, etc. Presenting these skills
as an offer of services will improve job search prospects, as employers are
not necessarily looking for precise transferable skills, but for what services
researchers can offer them. At the end of the training session, students will
learn to identify their key skills and to presenting them concisely as an offer
of services.
The one day workshop will cover:
Overview of your skills
Identifying your unique selling points
A systematic method to back-up your skills: the sales pitch
49
Chapter 6
Transforming and leveraging your scientific skills

Objective: Students will learn how to identify their key skills and transform
them into an offer of services.
Transforming your skills into an offer of service

Showcasing your skills in a job application
Showcasing your skills in a social network
Designing and using your elevator pitch

Date: Friday, 22 April, 09:30-17:30
Location: TBA
Credits: 7 hours
Validation: Students must attend the entire workshop to validate the hours
Google Classroom Registration Code: 17epsp
Frantastique and Gymlish: Online courses
Each morning youll receive an e-mail with an assortment of written content
and audio recordings. Each lesson takes ten minutes to complete and includes a story with dialogues, questions, mini-lessons and revisions.
After clicking the send button, youll receive your e-mail corrections with
your score of the day, explanations on why you got each question right or
wrong, transcripts of the audio recordings, the vocabulary you wanted to
learn more about, etc.
The next lessons will be customized according to your previous answers,
your expectations and your needs.
Credits: Variable based on number of lessons completed, each lesson is 0.25
hours
Validation: Students must submit their completion certificate with their annual
training report to validate the hours
Google Classroom Registration Codes
Frantastique: v09dzv
Gymlish: 6vtbqhv
Group language exchange/lessons: French and English
There has been increasing demand for in-person language lessons or a language exchange between native and novice speakers of French and English.
If you would like to improve your spoken French and/or English and are willing to help others, then this exchange is for you. The level of the course will
be up to the people interested - we may just meet periodically to talk over
beers, focus on science language specifically, or organize formal lessons. If
you are interested please register on Google classroom and we will plan the
course from there.
Coordinator: Sofie Leon
50
Dates/Location: To be determined based on number of students interested
Credits/Validation: TBD
Google Classroom Registration Code: o4dwj5
6.3 DIY your PhD curriculum

All FdV students are welcome to take a Do It Yourself (DIY) approach to
their PhD curriculum. This is especially true for the New Frontiers students
as their interests and needs are broad and may not be fully addressed by the
current FdV curriculum. We want students to be an active part of their PhD
training, so we encourage you to DIY your PhD curriculum.
The following are a list of options for New Frontiers students to participate
in while developing their custom curriculum. The FdV staff is available to
advise students through the process and to provide any support that may be
needed.
EdTech courses at the CRI

New Frontiers students are welcome to participate in any of the EdTech
courses, provided they get approval to join from the EdTech Director of Studies. Please contact Sophie Pne at sophie.pene@parisdescartes.fr for admission into the New Frontiers courses
21-25 Sept : MOOC (Yoni Dayan)

28 Sept-2 Oct : Serious Game (The Gamelab http://cri-paris.org/gamelab/)
Courses
The following courses may be of interest to New Frontiers students. Please
see the AIRE handbook for details and the EdTech calendar for course dates.

Serious Games (A. Taly, Gamelab)

Learning by doing (K. Lhoste, J. Chevrier)
New methods of scientific mediation (Les savanturiers, F. Taddei, G.
51
Chapter 6
Bootcamps
The intent with these bootcamps is to provide you with the framework (method, toolbox, strategy, a vision of the ecosystem and some network) you need
to achieve you own research or entrepreneurial projects. Moreover, since
you all come from different backgrounds we try to give you common practical
knowledge to feed your experimentations. While some of the subjects might
be familiar to you, others will probably be new and challenging. Luckily, you
are part of an interdisciplinary crowd, so there should always be someone
nearby who can help you out. This is one of the most important lessons at the
CRI: work together. The bootcamps available to New Frontiers students are:
Main- guy, R. Dubose, M. Marcel)

Philosophy of learning (S. Audidire, A. Janvier)
Technologies for learning (J-F. Bonnet, K. Lhoste)
Future education and learning society (S. Pne)
Open science and Citizen science (S. Mesmoudi, F. Cazalis, A. Berra, M.
Farge, V. Peugeot)
Create a White Course

Students are welcome to work together to create a course/workshop on a
topic of their choosing, for example: open science, innovative education, science and design, etc. In order to create a course, students would need to
contact and arrange for speakers and presenters. They are encouraged to
work with the FdV staff to make contacts with members of the CRI network.
A budget is available to facilitate such a course, please contact the FdV staff
for details.
Create a MOOC
In keeping with the DIY approach, students are welcome to work with the
MOOC factory at the CRI to a create an online course on a topic of their
choosing. A number of programs and resources are available for interested
students. Please contact the FdV staff for details.
Other workshops
A number of workshops are held by members of the CRI or its partners.
Many of these may be suitable for PhD training for New Frontiers students,
including:

Sage bionetworks
Night Science
Hello Tomorrow Challenge
iGamer workshops
World Innovation Summit for Education (WISE) events
Frontiers in Education (FIE) international conference
6.4 Student initiatives

Student led initiatives are a welcome and encouraged part of the FdV curriculum. Involvement in activities like CRI academic clubs and the FdV PhD
retreat can be validated as training hours.
52
Student clubs
Students have the opportunity to form clubs based on mutual interests during
the CRI Discovery Days. They will have access to a budget for club events.
Please contact the FdV staff for more information on how to form new clubs.
Previous FdV student clubs include:
WAX Science
Gamelier
In Vitro Artificial Intelligence
Retrospective and Visionary Talks
Fabelier
Synthetic Biology
Open Science School
PhD Symposium
The Paris Interdisciplinary PhD Symposium (PIPS) is an student-organized
event that aims to bring together researchers and Ph.D. students motivated
by the same spirit. It is an opportunity to meet new people from diverse elds
with a common interest in life sciences, sharing ideas and changing ones
own point of view on different issues. There have been two successful symposiums that took place in Paris in December 2009 and June 2011. Current
students are welcome to propose a new version of this event for the 20152016 academic year.
FdV PhD Retreat
Future editions of the FdV PhD Retreat are welcome and encouraged. Please
contact the FdV staff and FdV student representatives if you would like to be
involved in planning the next retreat!
53
Chapter 6
In May of 2015, the first FdV PhD retreat took place in Carry-le-Rouet, in
South of France. This was an opportunity for FdV students, staff, and alumni
to come together to reinvigorate the community. The 4 day retreat featured
scientific talks in the morning, social activities in the afternoons, and informal
meetups between all of the participants in the evenings. The hours spent at
the retreat related to scientific exchange will be validated as training hours.
7. Important Contacts
7.1 FdV PhD Program contact
Name
Email
Phone
FdV PhD Office
fdvphd@cri-paris.org
01 76 53 46 22
Franois Taddei
FdV PhD Director
francois.taddei@cri-paris.
org
francois.taddei@inserm.fr
01 76 53 46 01
David Tareste
FdV PhD Co-director
of Studies
david.tareste@cri-paris.org
01 57 27 80 38
Antoine Tesniere
FdV PhD Co-director
of Studies
antoine.tesniere@cri-paris.
org
01 58 41 14 89
Sofie Leon
FdV PhD
Scientific Coordinator
sofie.leon@cri-paris.org
01 76 53 46 16
Elodie Kaslikowski
FdV PhD Administrative Assistant
fdvphd@cri-paris.org
01 76 53 46 22
FdV Student
Representatives
students.representatives.
ed474@gmail.com
54
7.2 FdV Support and CRI contacts

Name
Email
Phone
Marlyne Nogbou
Management
Assistant
marlyne.nogbou@cri-paris.org
01 76 53 46 04
Tien Clabaut
Accountant
tien.clabaut@cri-paris.org
Vronique Waquet
General Services
Manager
veronique@cri-paris.org
01 76 53 46 20
Youcef Benarezki
General Services
youcef.benarezki@cri-paris.org
01 76 53 46 19
Nathalie Sussfeld
Human Resources
Manager
nathalie@cri-paris.org
01 76 53 46 03
Laura Ciriani
General Secretary
laura@cri-paris.org
01 76 53 46 09
Galle Chevalon
International Relations Coordinator
gaelle.chevalon@cri-paris.org
01 46 61 25 23
-->Contact Marlyne to book travel with FdV funds
01 57 27 80 38
--> Contact Tien to submit invoices and receipts for FdV reimbursement
55
7.3 Other CRI programs

AIV Masters
Program
masteraiv@cri-paris.org
01 76 53 46 25
EdTech Masters
Program
masteredtech@cri-paris.org
01 76 53 46 21
Licence FdV
Bachelor Program
licencefdv@cri-paris.org
01 76 53 46 24
Les Savanturiers
LOpen Lab
savanturiers@cri-paris.org
lopenlab@cri-paris.org
01 76 53 46 05
01 76 53 46 12
7.4 Paris Descartes University Contacts

Directeur de lInstitut de Formation Doctorale : Michel VIDAUD
Responsable administrative de lInstitut de Formation Doctorale :
Mariel FAYEMI : mariel.fayemi@parisdescartes.fr
BUREAU DACCUEIL ET DE SUIVI DES DOCTORANTS (INSCRIPTIONS)
scolarite.doctorat@parisdescartes.fr
01 76 53 01 12/ 01 13
BUREAU DE LORGANISATION DES SOUTENANCES
soutenances.phd@parisdescartes.fr
Gislaine MONTEBELLO
gislaine.montebello@parisdescartes.fr
01 76 53 01 14
Graldine VERON
geraldine.veron@parisdescartes.fr
01 76 53 01 15
BUREAU DE LA GESTION ADMINISTRATIVE DES CONTRATS PARIS DESCARTES (Contrats
doctoraux Paris Descartes, CDD, Mission Enseignement et Mission Hors Enseignement)
ifd@parisdescartes.fr
01 76 53 01 16
FORMATION DES DOCTORANTS A LINSERTION PROFESSIONNELLE - MISSIONS COMPLEMENTAIRES (Responsable du Comit Paris Descartes)
ifd@parisdescartes.fr
56
7.5 Paris Diderot University Contacts

Responsable administrative de lInstitut des coles Doctorales :
Galle LE CAMUS : gaelle.le-camus@univ-paris-diderot.fr
BUREAU DACCUEIL ET DE SUIVI DES DOCTORANTS (INSCRIPTIONS)
jocelyne cabald : jocelyne.cabald@univ-paris-diderot.fr
01 57 27 54 26
57
FdV PhD
2015 - 2016
Centre de Recherches Interdisciplinaires

8-10 rue Charles V, 75004 Paris
www.cri-paris.org/doctoral-school-fdv

FDV 2015 2106 Program

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COLE DOCTORALE

2015-2016 Program Handbook

cole Doctorale Frontires du Vivant (FdV)

Dear FdV PhD Student,

2. FdV Program guidelines

1.1 Life sciences

3. Thesis advisory committee guidelines

4. Annual Training Report

6. FdV Training Program

4.1 Online Platform 

Required FdV courses and workshops

1. About the FdV program

1.1 Life sciences

1.2 Education and discovery

2.1 FdV spirit

2.2 Admission to the PhD program

2. FdV Program guidelines

2.3 Training program

Annual Training Report

2.4 Thesis advisory committee

2.5 Criteria for doctoral degree

2.6 Duration of the thesis

2.7 Post-thesis preparation and follow-up

participate in and maintain an FdV alumni network.

2.8 Signatures and acknowledgments

2.9 Website representation and student network

Student website profile

Scientific ethics and responsible conduct

3. Thesis advisory committee guidelines

3.1 Tutor selection

3.2 Thesis Summary Report (TAC Report)

For 1st year candidates the summary is intended as an updated thesis

3.3 TAC Meeting and Tutors Report

3.4 Submission of TAC Reports

3.5 TAC Budget

4. Annual Training Report

4.1 Online Platform

6. FdV Training Program

2. Interdisciplinary Fridays Seminars

3. Oral Communication and Public Speaking, choose one:

General Public Speaking

Engaging scientific presentations

Scientific presentations for a non-scientific audience

4. Critical Analysis of Research Articles

5. FdV/AIV Thematic Workshops

6. Written scientific communication, choose one:

Alternative Written Scientific Communication

7. Well-being, integrity, and responsibility in research intro session

8. Well-being, integrity, and responsibility in research practical session, choose one:

Managing scientific collaborations: Integrity, negotiation and

Best DOC: Well-being, health, and work for the doctorate

Responsibility in research and entrepreneurship

1. Creating Interdisciplinary Research Projects Workshop

6.1 Required FdV courses and workshops

Requirement 1: Creating Interdisciplinary Research Projects Workshop

The specific aims are:

Requirement 2: Interdisciplinary Fridays Seminars

Coordinator: Sofie Leon

2. FdV Program guidelines

1.1 Life sciences

3. Thesis advisory committee guidelines

4. Annual Training Report

6. FdV Training Program

4.1 Online Platform

Required FdV courses and workshops