research Science technology

Open Source: Zotero (reference manager)

Zotero is a free and open-source reference management software to manage bibliographic data and related research materials (such as PDF files). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes, and bibliographies, as well as integration with the word processors Microsoft Word, LibreOffice Writer, and Google Docs. It is produced by the Center for History and New Media at George Mason University.

Wikipedia contributors. (2020, January 8). Zotero. In Wikipedia, The Free Encyclopedia.

Now that Mendeley is encrypting all of your libraries on your own computer, it might be worth looking for an alternative reference manager. Zotero has everything that you’d expect from a reference manager:

  • Importing of all kinds of resources (not just PDFs) via a browser plugin.
  • Automated extraction of resource metadata during import.
  • Notes and tags for resources.
  • Exporting of libraries in multiple formats.
  • Citation management in MS Word, Google Docs, and LibreOffice Writer.
  • Cross-platform (i.e. it runs on different operating systems) with the ability to sync between devices.
  • A browser-based version of your library that you can access when you’re not at your computer.

In addition to the standard features listed above, Zotero also has the following:

  • It’s open-source, which means that you’ll always have a version available for you to use, regardless of what happens to the current developers.
  • A plugin database that enables developers to create custom features that most users probably won’t need but which might be valuable for some.
  • It supports more than 30 languages.
  • Ability to create relationships between resources.
  • The developers are always working to figure out how to make your life easier as an academic and researcher (see Tweet below).

Here is a more comprehensive overview of what Zotero offers (including some of the main differences with competing software), here’s the blog where you can stay updated with development of the programme, and the Wikipedia page with some additional background and context.

If you use Mendeley, Paperpile, Endnote or any other reference manager and aren’t quite happy with any aspect of it, you might consider giving Zotero a go.

Note: This is a new experiment on the blog where I’ll share some of the open-source software that I use. Partly because I believe in the idealogy that drives open-source project development but mostly because I actually think that the open-source alternatives are better and would love for more people to use them.

research social media

Mendeley: research paper / PDF management

A little while ago I wrote about Zotero and how I felt it came short of my expectations for a reference manager (my main contention was that it wasn’t very efficient at managing my offline content, for example, PDFs.  Incidentally, see this interview, which also mentions this shortcoming of Zotero).  Today I came across Mendeley, which at first glance seems to fulfil all of my PDF management requirements.  It’s still a beta release, so expect some bugs and stability issues.

First of all, Mendeley is both a desktop tool that’s cross-platform (major bonus points already) and web service, running locally and syncing documents and metadata to a remote server.  This has the advantage of being both a backup and online library that you can access from any internet-enabled computer.  The company provides 500 MB of storage space for members which, while not big enough for everyone, will suffice for most people.

Unlike some services that are jumping on the “social media” bandwagon and are useless, it’s inclusion in Mendeley adds a powerful incentive to use the tool.  With an emphasis on collaboration in research, the ability to locate and share information with like-minded people is a great idea.  It allows a user to search for other academics / researchers who are participating in similar work and enables the sharing of resources or collaborative work.  Users can make their entire library public, or only certain parts of it, and the software will attempt to match similar articles and recommend other members based on extracted metadata and the papers in their libraries.  Privacy concerns mean that this will be an opt-in service, rather than enabled by default.

I like the potential of Mendeley’s recent announcement concerning collaboration with CiteULike, which will allow users to integrate data from both services into one place, and share the results with others.  The company has also developed a bookmarklet that allows users to automatically import citation information from appropriate sites (e.g. PubMed) straight into your Mendeley library.  I also love that Mendeley will monitor folders and automatically add the relevant metadata into your library when you add new resources to a folder.  Another interesting feature are the “vanity statistics” (my term for it) that will enable the software to generate individualised stats on your research papers / publications based on who’s reading them.  It’s this attention to detail, as well as the social networking tools that set Mendeley apart from other document managers.

All in all, it seems like Mendeley is a great tool for managing PDFs, and the social networking aspect adds an interesting dimension to the process.  I’ll still use Zotero in the way that I have been (i.e. for working through and annotating academic content online, usually in blog form), but it seems likely that Mendeley will become the standard tool for managing my PDF library.