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Tools to collaborate in science: reference manager software

Posted By Connections Editor, Monday, June 30, 2014
Updated: Wednesday, June 25, 2014
Eugenia (Kena) Flores-Figueroa, Peter van Galen, Konstantinos Kokkaliaris, Sofie Singbrant and Teresa Bowman.

In our last issue of Connections, we discussed collaborative science and the importance of clear communication with your collaborator. Collaborations will not only include sharing samples, methods and ideas, but can also lead to co-authored grants, proposals or manuscripts. Without the proper technology, these collaborative writing projects could be a headache, leaving you with an inbox full of papers and drafts. Sharing and working on common documents is now much easier, thanks to a flurry of new technology. Here we will discuss some of the pros and cons of various reference managers and how best to utilize these tools for an effective collaboration.

Reference manager software is software for storing, organizing, sharing and using bibliographic citations. This kind of software allows multiple authors to add citations, download papers and add comments. Whether you are a pro or a newbie, the number of applications on the market can be intimidating, so we compared some of the reference manager applications to help you find the software that works best for you. When choosing the right software, you should consider cost, operating system compatibility, remote access, storage capacity, integration with your word processor (Word, Open Office…), reference styles and if it allows sharing and collaboration. It is also important to consider if it is user friendly or intuitive, as you do not want to spend too much time learning how to use it.

For a quick comparison, check out our comparison chart: 

MekentosjThomson Reuters
Operating systemPC, Mac and LinuxPC, Mac and LinuxPC and MacPC and MacPC and Mac
First public relase200820062007Late 1980's2014 for full version
Costfree (up to 2 Gb online storage)free (you can upgrade your storage capacity by a cost)$79 (students $45)$249.95 (students $113.95)free (pro version t.b.a.)
Application for smart phoneyesnot from Zotero but you can use Papershipyesno but there is an iPad appiPad app coming Jan. '14
Intuitive softwareyesyesyesyesyes
Citation styles43116770 +Many + add your own5000+Over 530
Sharing bibiographyyesyesnoyes (private groups)no
Best featureFull text search throughout papers / PDF annotation incorporated / Social networking allowing users to share librariesFriendly software, you add your citation with one mouse click. It is great for collabroation.Intuitive user interface yet many customization options / Remembers university proxyUser-friendly reference manager that allows you to attach and search full text PDFs Very slick, requires no setup time
Worst featureproblematic integration with academic databasesyou can not annotate your pdfs and it does not have an app on its ownMany issues with their latest update (Papers 3)The annotation features are not very good and the licence is expensive Some features are missing
Export file formats.bib .ris or Endnote .xml formatRDF, TEI, Wikipedia citation templatesBibTeX, Endnote, RefmanText only, rich text format (rft), html and Endnote (xml)none
Import file formats.xml (endNote format), .bib, .risris file formatBibTeX, CiteULike, Endnote, Pubmed, RefmanMtiple formats including Endnote (xml), Pubmed, Reference manager (ris) and PDFnone
Word processor integrationWord and Open OfficeWord and Open OfficeWord and PagesWord, Pages, Open OfficeWord (beta version)
Database conectivitypotentially problematicDropbox integration (Papers 3) is fussyyesso far always get "Sync Error"
In-app search with university proxy integrationnoyes and for some can be problematic when the institution requieres web-based authentication, they are working on that problem.yes (remembers login and works smoothly)yesyes (have to log in frequently)

Endnote (
Endnote is about 20 years older than the other reference managers we tried: the first Endnote software review is from 1989! It has stood the test of time with a robust set of features. Endnote is a user-friendly software that doesn’t take long to get started with. It allows you to import and export references in several different formats, and has over 5000 citation styles that can easily be further customized if needed. The addition and management of citations and the reference bibliography in Word is very straightforward. However, insertion of citations in powerpoint is so far only available for Windows and not for Mac. Regarding PDF-files, Endnote can both find and incorporate reference information for a PDF you already have (as long as it has a DOI number), as well as find and attach a PDF-file for a reference already existing in your library. Both references and papers can be organized in folders and searchable smart folders, and the program also allows you to search full text PDFs. However, the annotation features in Endnote are limited. But the biggest drawback is perhaps the price, since Endnote is by far the most expensive reference manager software covered in this review. Apart from the annotation feature, Endnote is a very good reference manager, but we think the price tag will make a lot of users start looking at the cheaper options.

Papers (
Papers is a fully featured PDF- and citation manager. You can do everything in Papers, from searching many online databases to annotating files. When searching for papers, the program remembers and automatically uses your university proxy. When you download papers, the PDFs get automatically named and downloaded to a folder structure you can set. Within the program, papers can be organized by tags, keywords, in smart folders, etc. Changing paper annotations is easy. Managing references in Word is easy and pasting references in Powerpoint, emails or anywhere is effortless. The only missing feature of Papers 2 is syncing between computers. Dropbox syncing has come with Papers 3; however, from our experience, Papers 3 beta was a disaster with many bugs and a library that was not accessible through Finder. The official release of Papers 3 is better: certainly worth a try if you want to be able to set up a customized workflow.

Readcube (
The new kid on the block is Readcube. Moving beyond its origins, this PDF manager just got updated to manage citations and sync papers in the cloud ( An iphone and iPad app is available now, which eliminates the need for any other software. Searching Pubmed, Google Scholar or your own library within the app works really smoothly. You can download enhanced PDFs, which puts references within 1-click reach. Readcube’s user interface is extremely clean, which is great, but some features are missing. For example, you currently can not change individual fields in paper annotations or set automatic naming of downloaded PDFs. However, if you want simple software that requires no setup and works smoothly, consider giving Readcube a try. The developer team is working to add more features while maintaining sleekness, and we are excited to see where Readcube is going.

Mendeley (
Mendeley is a tool for organizing academic research papers, creating/sharing libraries, and generating citations and bibliographies. It has two formats (the downloadable program available for Windows, Mac, Linux and the web-based software compatible with all web browsers) and two versions (basic/free and premium). Its main features include: automated extraction of metadata information from PDF-papers and databases, PDF annotation (highlight text and sticky notes), text search function and export of citations and bibliographies in document processing software (Microsoft Word, OpenOffice, LibreOffice). One of its unique features is the social network module allowing users to create and share online libraries with other users (users can choose between creating private or publicly available libraries), while getting article recommendations. Mendeley offers a larger storage space (2GB) compared to its rivals and allows synchronization between different computers and operating systems.
Originally created by three German PhD students in 2007 (first software version was released in August 2008), Mendeley has won several awards, such as the ‘’European Start-up of the Year 2009’’ and has been ranked 6th in Guardian’s ‘’Top 100 tech media companies’’, before being bought by the publishing company Elsevier. Despite the growing number of users (almost two million), Mendeley has some drawbacks compared to other PDF and citation managing software. In particular, it often has problematic integration with academic databases (compared to Refworks), since entries often require manual inspection and correction. Also, book citation requires further development (inferior to Zotero and Endnote). Finally, the PDF annotation module offers only basic functionality (compared to Zotero) and the optical character recognition function is not yet available.

Zotero (
Zotero is a free, friendly and intuitive software to collect, organize and cite, and works great for collaborations. We recommend this software for the “newbies” as the online tutorial (offer on their website) is brief and it’s just what you need to start using it. As with the other reference managers, there are also a lot of tutorials available on youtube.
One of its best features is that is very easy to collect your information; your library will displayed on the bottom of your search engine (it works great with firefox, and now you can also use other search engines), so when you find a reference on pubmed or on the ejournal, within one mouse click you get the reference integrated into your library (and if you get access to the paper, or it has free access, it also saves the paper into your library.
You can collect anything, from papers, audio, video, books, images and webpages. You can add notes to your files, so you can use the note to write the citation of the paper, or the information that you will use from that paper. This helps to organize your bibliography, PDFs and notes so it is really smooth to write. You can organize papers by title, author, year and you can also search within the document. What we value most from this software is how easy it is to collaborate and write a paper with two or more people. All the collaborators can access the same library and add citations on the same document; you can decide who can only view or edit the library. It does not have an app on it own, but you can sync your Zotero (and also Mendeley) account using Papership (, which is an application available at the iTunes store that is designed to give you access to Mendeley and Zotero libraries on your iPad or iPhone. You can annotate your PDFs and share them.

1. Mendeley, official web site (
2. Wikipedia (
3. Office Information Technology, University of Colorado Boulder (
4. Academic Technology blog (
5. Stephen Miller "EndNote." Computers and the Humanities, vol.23 (1989) pp. 489-491

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