Adopting reference management software

Compiling a bibliography is an inevitable part of the process of writing an article or a thesis, and it can become a real headache if left to the last minute ("I'll deal with that later when I have time...")!
Managing bibliographical references from the very beginning of the research process, with the appropriate tools, is generally much easier and less time-consuming than you may think – and it is very handy later on.

Choosing your reference management software

The aim of reference management software is to simplify the task of managing references when writing an article or a thesis. It enables you to compile a personal or shared database containing all the references you collect during your research. Later on, when you begin the writing process, the software helps you to format them easily in line with the instructions for authors.

We have created a handy comparative guide of the different reference management software available

This is the most comprehensive software, even if it is less intuitive than others. It is one of the oldest commercial reference management programs. It is currently developed by Clarivate Analytics. The most recent version (currently x9) is available for all the library's users on the reading room computers.


Resources on the EndNote website


EndNote website

The easiest to use and the only completely free reference management software. It can be used to import all document types. But changing styles is relatively complicated, your library can soon become a bit messy and it doesn't allow you to annotate PDF files. It is the most widespread open source reference management software.


Resources on the Zotero website


Zotero website

The most intuitive, user-friendly software for managing PDFs, even if changing bibliography styles is quite complicated. It is a commercial reference management tool that was originally developed by students at a US university to manage their PDF files. It now belongs to the publisher SpringerNature.


Resources on the Papers website


Papers website


The first to propose networking features to researchers, but it cannot automatically import PDFs.

It is freemium software, meaning that it is free of charge but some features can be improved by paying. It currently belongs to the publisher Elsevier.


Resources on the Mendeley website


Mendeley website

This is a shareable workspace where researchers can work on articles that interest them (with features including sharing and annotation).

It belongs to Faculty of 1000, a publisher of services. This software, which usually requires a paid subscription, is accessible free of charge to anyone with an account.


Resources on the Sciwheel website


Sciwheel Website


Here are some more reference management software options



Managing your references

Setting up automatic updates

To make sure you get the most out of these tools, your references need to be correct and up to date. Bibliographic databases and publisher websites can help you by allowing you to save your searches and receive regular email updates for them. The My NCBI tool in PubMed is one example. All you then need to do is import these results into your preferred reference management software.

Mettre en place sa veille bibliographique - Bibliothèque du CeRIS - Institut Pasteur

Le saviez-vous - Bibliothèque du CeRIS - Institut Pasteur

If you need to perform a one-off search,we would recommend that you use a publisher database or website rather than your reference management software. The search engines in reference management software are not always very powerful and can generate large numbers of irrelevant results. Many publisher databases and websites have also developed highly effective export tools.


Questions & Answers

Can the library produce my bibliography for me?

We can guide you in formulating your search query and using the various tools available to find relevant references for your bibliography. We can also help you choose and use appropriate reference management software.

I'm lost with all this reference management software. How can I choose the tool that is best suited to my needs?

First of all, take a look at our reference management software comparison guide. You can also come to the reading room in the library and ask us for additional guidance. And if you are a member of the Institut Pasteur in Paris or the Institut Pasteur International Network, you are welcome to take part in the workshop "Bibliographic tools – hands-on session".




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