My search for the best reference manager

Finally, I think I found what I need for my Bibliography management and referencing combination.

My requirement (typically of many researchers) is that I need to do collaborative writing with people using MS Office tools alone, while LaTeX becomes a preferred option for myself involving many equations. I am by now very much used to MS Word and LO Writer; but still LaTeX feels very comfortable in (1) handling figure placements and captions (I can push them to the end  or keep them in-line with just one preamble command) (2) easily changing citations and citation styles between different journals, and (3) equation typing and referencing. The biggest drawback is that LaTeX does not have an easy-to-use collaborative writing feature like the in-line commenting and review options of Word. Here, the LO Writer and Word are extremely handy, and the need for this feature cannot be understated.

There are many ways for managing bibliographies, referencing and automatically changing the bibliography style in Word or Writer either by using inbuilt referencing system or with external add-ons with just a few clicks. Using internal referencing system needs either building the whole bibliography data by typing from scratch or exporting this data into a suitable format to be imported into Word or Writer. Many reference managers like Mendeley, Zotero, JabRef, etc. manage the literature database and provide plugins for MS Word or LO Writer. Moreover, these reference managers (or their plugins) allow to easily change between the citation styles just with a few mouse clicks.

Here is my personal experience. I have experimented with Mendeley and JabRef+Drropbox for reference management and syncing between non-homogeneous devices (an office Linux desktop, a laptop, and my Android tablet).

So what’s the problem? My problem is I work on both Windows and Linux platforms and use documentation tools like LibreOffice Writer, LaTeX (Kile), and MS Word. I keep writing and synchronizing literature and documents between several devices. On my Linux laptop, I use Windows inside VirtualBox exclusively to take OneNotes, prepare PowerPoint presentations, and do some collaborative writing/reviewing. These are the three cases where there is still no matching alternative in the Linux environment yet (I am sure many would agree with me on this), and therefore I am forced to use a virtual machine.

I use Dropbox to sync among computers and a tablet.

I have been using JabRef for a longtime and really like its integration with Kile and LibreOffice Writer; JabRef directly inserts citations into Kile or Writer. JabRef can save the database in BibTeX format, so I can also use this file with any preferred LaTeX work flow.

Mendeley has no integration with Kile, but can save in a .bib format.

Mendeley has clients for Windows and Linux. However, it stores its processing information about the database in external files located in some local database and configuration files that are specific (I guess) to OS. So syncing between devices is through its cloud based system only, leading to multiple copies/instances when using shared folder/drives in VirtualBox or dual boot environments. In contrast, JabRef supports relative file paths and platform-independent file link mechanism, so the same .bib file can be accessed through both the Linux and Windows clients. Moreover, JabRef does not store any data (except for configuration) in other machine-specific auxilliary data folders, so all I need is sync my .bib file and the folder containing bibliography sources (PDFs, docs, odt, PS, …).  Perfect for shared folders/disk in a dual boot or VirtualBox environment!

For Android, there is a free JabRef-compatible (nearly a clone) app called RefMaster. Mendeley also has an app for Android, which I haven’t used so far.

Both JabRef and Mendeley have plugins for LO Writer…

JabRef has a MS Word plugin called BibTeX4Word, while Mendeley has its own. Here has been my biggest difficulty so far. BibTeX4Word requires a working latex system like MikTeX. Installing this is not a big deal, I did it on Windows in VirtualBox. Used BibTeX4Word in several internal documents and journal manuscripts-worked like a charm. But the problem came when I had to use a specific journal’s (Acta Materialia) bibliography style file in a Word document. The result of BibTeX4Word was a mess, and no native latex style files matched with the journal specification. So I had to use the closest and then edit all the references manually. I had to do this again before submitting a revised manuscript. Thank God, it was only one revision! I had similar difficulties with my another previous manuscript in Word. This is when I have started experimenting with Mendeley. Mendeley seemed to be the solution as it has inbuilt support for many up-to-date journal citation styles, and it only needs a couple of mouse clicks to change to the correct style. However, I could not use the same .bib file for both JabRef and Mendeley since they use different custom keys for storing additional info like file location, etc. So Mendeley required me to install it on both Linux host and Windows guests, to use the online syncing for the database. This is when I started considering switching to Mendeley.

Apart form the above drawbacks of Mendeley against JabRef, Mendeley neither stores editable annotations inside PDFs, nor allows me to open the document in external viewers of my choice. This is a obstacle for me, since using Mendeley’s inbuilt annotation system means I have to stick with it forever with it and only can see annotations inside it! So my search continued…

Then I came across Docear! Docear presents itself as more than a reference manager, containing brain-mapping software to take notes that nicely integrates with annotations in PDFs, can embed images, LaTeX formulae, cross-referencing with other database articles, and more… It embeds JabRef, and calls external programs for PDFs. The annotations created there can be linked in the brain-maps created in Docear. This is definitely an attractive feature! But it is not the most attractive feature for me at the moment. It is the MS Word plugin for BibTeX databases-the Docear4Word! Docear itself saves the database in .bib files (naturally since its reference manager is basically JabRef). However, to use the Word plugin, one does not need to use Docear, but any reference manager that can export to a .bib file can be used independently. And the word plugin uses citation style sheets based on .csl format that can be downloaded from or from Zotero’s web site. It is also possible to create your .csl file on the page by simply typing in the format. The Word plugin automatically reformats the style with just a mouse click.

Seems like I found the perfect solution for my problem. Now I have uninstalled Mendeley, BibTex4Word+MikTeX. Now I can work with Kile/JabRef, JabRef/Word+Docear4Word, or JabRef/Writer+JabRefOOPlugin using a single data store and single .bib file on my laptop with VirtualBox and sync with Dropbox to other devices!