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Writing and defending your thesis
Preparing the administrative thesis-defence dossier requires the same rigour as preparing the thesis defence itself. This dossier cannot be completed in a hurry. The conditions for authorisation of the defence are presented in the Doctoral School's regulations.
The doctoral school shall grant authorisation to defend their thesis to those applicants who fulfil the following criteria :
Note : requirement of minimum of 80 hours of additional training including training « intégrité scientifique » & « Ethique de la recherche »
- The summary of the publications from the thesis work :
- Refer to the provisions specific to the enrolling institution (cf. box) to start the application.
- The doctoral student must contact the Doctoral School at the following address secretariat-NSCo@univ-lyon1.fr with :
- the composition of the defence jury and referees signed by the thesis supervisors
- the training report which can be downloaded from ADUM and exemption request form if applicable
- the training report which can be downloaded from ADUM and exemption request form if applicable
Note : requirement of minimum of 80 hours of additional training including training « intégrité scientifique » & « Ethique de la recherche »
- The summary of the publications from the thesis work :
One of the following two conditions must be satisfied :
Option 1 : at least one accepted publication as first author or under review publication as first author in an international journal. The manuscript of which is available in open access. The publication(s) must deal with the thesis topic.
Option 2 : one publication not yet published but available in preprint and an accepted publication in the format of a Registered Report or Data Paper. These documents must deal with the thesis topic.
Option 1 : at least one accepted publication as first author or under review publication as first author in an international journal. The manuscript of which is available in open access. The publication(s) must deal with the thesis topic.
Option 2 : one publication not yet published but available in preprint and an accepted publication in the format of a Registered Report or Data Paper. These documents must deal with the thesis topic.
Consult the FAQ
How do I put my manuscript in the open access ?
There are two possibilities :
• the journal in which the article is published is an open access journal: in this case there is nothing more to do, the article will be accessible by anyone interested. A directory of open access journals is available here : https://www.doaj.org
• the article is not yet published or the journal is not open access: in this case, it is possible to deposit the manuscript (before publication!) on a public online archive such as arXiv, BiorXiv, PsyArXiv, MedRxiv, or on the French institutional site HAL.
How many does it cost ?
There too it depends on the site :
• on public or institutional archive sites: no cost
• for open access journals: some are free (Diamond model, for example PeerCommunity), but others charge an article processing charge (APC). The DOAJ directory allows you to filter newspapers by this criterion. Some subscription journals (especially among the most reputable ones) operate with a "hybrid" system: they are not "open" but charge an additional fee to authors to put a new article in "open access". Choosing this solution means paying twice (subscription and open access), and it is then preferable to put the "author-accepted manuscript" on an open archive (HAL, BiorXiv, ...) knowing that the journal sometimes imposes an embargo which cannot exceed 6 months (but see here how to avoid this embargo).
• note that some publishers sign "transformative agreements" with institutions to lower the cost of publication per article (which is in fact directly paid by the institution). For example this agreement between Couperin (a consortium of French academic and research institutions) and the publisher Wiley. This type of agreement is not yet very frequent but it is important to watch out for them.
Won't my thesis work be devalued if it is published in open access ?
A common fear of open-access publishing is that these journals are less selective and demanding on the content of articles and that their content can be less trusted. However, while there are indeed so-called "predatory" journals whose sole purpose is to attract people willing to pay to be published, there are also open access journals that do a very good job of peer review. Some of them are even of very high quality like PLOS Biology or eLife. Whatever the journal, it is up to the author to pay attention to the reputation of the journal and to what he/she generally finds there (B!son is an example of a tool that helps to choose a suitable and quality journal). Note that, if one does not wish to restrict oneself to open-access journals, the dissemination of the manuscript before publication on open archives remains a simple and efficient way to disseminate one's work to all (see above).
What a registered report ?
A registered report is an article that is submitted with only the introduction and methods. The peer-reviewing process will therefore only focus on its scientific interest and the expected quality of the experiments and analyses. Beware, this requires a lot of work to describe in great detail the protocol and the analyses and the statistics that will be done. Once the registered report has been accepted, the experiments and analyses must be carried out, and after verification that the experimental plan has been followed, the journal will publish the results whatever they are, without any other request. It is therefore much easier to publish results that turn out to be negative with this type of article. It should be noted that registered reports are nowadays more adapted to experiments that have precise hypotheses to be tested, but that an unexpected observation during the experiment can be published in the registered report in a special section that specifies that the experimental plan is not being followed. Here are some examples of generalist journals that offer this type of publication : Nature Communications, PLOS Biology, eNeuro, PLOS One, Scientific Reports (more complete list here)
What is a data paper ?
A data paper is a peer-reviewed article, published in a traditional journal, that describes a dataset that is generally open access. Formatting data, cleaning them and providing exhaustive metadata requires a substantial effort that is then valued by this type of publication. Anyone who uses the data later can cite the data paper.
Here are some examples of journals offering this type of publication : Scientific Data, GigaScience (more complete list here)
How to learn more about open-science ?
• On the government website : the Open science Passeport, a simple and concise guide for PhD students, and more generally the website Ouvrir la science
• Another FAQ on open access publications here
• Another FAQ on preprints here
• Another FAQ on registered reports here
• Another FAQ on data paper here
• An updated list of likely "predatory" journals : Beall’s list
There are two possibilities :
• the journal in which the article is published is an open access journal: in this case there is nothing more to do, the article will be accessible by anyone interested. A directory of open access journals is available here : https://www.doaj.org
• the article is not yet published or the journal is not open access: in this case, it is possible to deposit the manuscript (before publication!) on a public online archive such as arXiv, BiorXiv, PsyArXiv, MedRxiv, or on the French institutional site HAL.
How many does it cost ?
There too it depends on the site :
• on public or institutional archive sites: no cost
• for open access journals: some are free (Diamond model, for example PeerCommunity), but others charge an article processing charge (APC). The DOAJ directory allows you to filter newspapers by this criterion. Some subscription journals (especially among the most reputable ones) operate with a "hybrid" system: they are not "open" but charge an additional fee to authors to put a new article in "open access". Choosing this solution means paying twice (subscription and open access), and it is then preferable to put the "author-accepted manuscript" on an open archive (HAL, BiorXiv, ...) knowing that the journal sometimes imposes an embargo which cannot exceed 6 months (but see here how to avoid this embargo).
• note that some publishers sign "transformative agreements" with institutions to lower the cost of publication per article (which is in fact directly paid by the institution). For example this agreement between Couperin (a consortium of French academic and research institutions) and the publisher Wiley. This type of agreement is not yet very frequent but it is important to watch out for them.
Won't my thesis work be devalued if it is published in open access ?
A common fear of open-access publishing is that these journals are less selective and demanding on the content of articles and that their content can be less trusted. However, while there are indeed so-called "predatory" journals whose sole purpose is to attract people willing to pay to be published, there are also open access journals that do a very good job of peer review. Some of them are even of very high quality like PLOS Biology or eLife. Whatever the journal, it is up to the author to pay attention to the reputation of the journal and to what he/she generally finds there (B!son is an example of a tool that helps to choose a suitable and quality journal). Note that, if one does not wish to restrict oneself to open-access journals, the dissemination of the manuscript before publication on open archives remains a simple and efficient way to disseminate one's work to all (see above).
What a registered report ?
A registered report is an article that is submitted with only the introduction and methods. The peer-reviewing process will therefore only focus on its scientific interest and the expected quality of the experiments and analyses. Beware, this requires a lot of work to describe in great detail the protocol and the analyses and the statistics that will be done. Once the registered report has been accepted, the experiments and analyses must be carried out, and after verification that the experimental plan has been followed, the journal will publish the results whatever they are, without any other request. It is therefore much easier to publish results that turn out to be negative with this type of article. It should be noted that registered reports are nowadays more adapted to experiments that have precise hypotheses to be tested, but that an unexpected observation during the experiment can be published in the registered report in a special section that specifies that the experimental plan is not being followed. Here are some examples of generalist journals that offer this type of publication : Nature Communications, PLOS Biology, eNeuro, PLOS One, Scientific Reports (more complete list here)
What is a data paper ?
A data paper is a peer-reviewed article, published in a traditional journal, that describes a dataset that is generally open access. Formatting data, cleaning them and providing exhaustive metadata requires a substantial effort that is then valued by this type of publication. Anyone who uses the data later can cite the data paper.
Here are some examples of journals offering this type of publication : Scientific Data, GigaScience (more complete list here)
How to learn more about open-science ?
• On the government website : the Open science Passeport, a simple and concise guide for PhD students, and more generally the website Ouvrir la science
• Another FAQ on open access publications here
• Another FAQ on preprints here
• Another FAQ on registered reports here
• Another FAQ on data paper here
• An updated list of likely "predatory" journals : Beall’s list
The language used for the thesis paper and its defence
The thesis should be written in french. Depending on the rules laid down by each university, permission may be granted for the thesis paper to be written in english. In the case of jointly supervised theses or theses with the "European Doctorate" label, all corresponding rules, regulations and agreements must be followed.
In all cases, it is imperative that you consult the rules specific to each institution.
In all cases, it is imperative that you consult the rules specific to each institution.
Choosing the date and venue for the thesis defence
It is up to the thesis director to propose a thesis defence date, at least 2 months prior to the proposed date.
Keep in mind that if you are a PhD student registered for the Y-1/Y academic year, your defence must be held no later than 31 December of year Y. A thesis defence scheduled for 1st January or later of year Y+1 necessitates your re-registration for the Y/Y+1 academic year.
Should you need to register for a 4th year, you will need to obtain special permission to do this, in line with current rules and regulations (see the section "Annual regristration" of the menu "During your PhD").
The thesis defence is normally held at the PhD student's institution of registration, though exceptions may be made with the approval of the head of the institution (contact the doctoral studies department to validate a location outside the university). For jointly supervised theses, the defence location is specified by common accord in the "co-supervision agreement".
Keep in mind that if you are a PhD student registered for the Y-1/Y academic year, your defence must be held no later than 31 December of year Y. A thesis defence scheduled for 1st January or later of year Y+1 necessitates your re-registration for the Y/Y+1 academic year.
Should you need to register for a 4th year, you will need to obtain special permission to do this, in line with current rules and regulations (see the section "Annual regristration" of the menu "During your PhD").
The thesis defence is normally held at the PhD student's institution of registration, though exceptions may be made with the approval of the head of the institution (contact the doctoral studies department to validate a location outside the university). For jointly supervised theses, the defence location is specified by common accord in the "co-supervision agreement".
Composition of the jury
The thesis director will submit his or her propositions for a jury to hear your thesis to the president or head of the student’s institution of registration, usually at the same time as the student proposes a list of referees.
The composition of a jury to hear a thesis defence must obey strict rules laid down by the university.
Each institution may also have specific requirements regarding the composition of the jury defence committee; contact your institution for more information.
Once all necessary checks have been made and all reports received, the head of the PhD student's institution will sign the authorization to proceed with the thesis defence. Official notification of the thesis defence will then be issued and the jury members convened.
The composition of a jury to hear a thesis defence must obey strict rules laid down by the university.
Each institution may also have specific requirements regarding the composition of the jury defence committee; contact your institution for more information.
Once all necessary checks have been made and all reports received, the head of the PhD student's institution will sign the authorization to proceed with the thesis defence. Official notification of the thesis defence will then be issued and the jury members convened.
Specific provisions by each institutions
The authorization to defend is accorded by the head of the establishment after consultation with the doctoral school. The procedures for the defense are defined by the Arrêté du 7 août 2006 and by certain rules specific to each university. The doctoral studies department manages the defense and the delivery of the diploma. This is why we invite you to refer to the website of your enrolling establishment for more information on the calendar and the steps of the constitution of your request.