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Open Source Reference Manager


Sometimes I feel that Open Source has a critical dependency: the user. And sometimes I feel that users deserve the software they choose to use, and the conditions attached to it. Last week I had one of these days.

01-ms_office_ribbon

A customer asked me to solve a mysterious problem: Microsoft Word 2007 with Reference Manager 12 crashed, and then Reference Manager was completely unavailable, even after re-installing both. This university lab has been a good customer for four years now – server side. Client side, besides the one exception (who runs Windows in VirtualBox), they barely tried Firefox.

Scientist write. They write a lot and they cite a lot. They need a database of references, and they must format them to the specifications of the journal where they will be published. In this lab, Reference Manager is king. A proprietary solution, owned by information technology giant Thompson Reuters (who conveniently also owns “competitor” EndNote).

After a little bit of fiddling, and against every documentation I found on the web, I found that Microsoft Word has an aptly named registry key: Resiliency/DisabledItems. It has decided that it does not work with Reference Manager 12.0.1 and put it on a black list. Forever. The only solution was to delete the registry key!

03-win_registry_hack

Even in light of this obviously intentional bug that handicapped half the lab for two weeks (they tried internal IT before calling me): They still insist using Microsoft Office, because Reference Manager does not work with OpenOffice. And they insist using Reference Manager. Their principal fears are the lack of support and the loss of the database they have built over more than a decade. I was unable to articulate to them that their biggest risk is to have their data locked into a proprietary format.

I’ve searched the web and found a few open sourced reference managers. But I have no experience and also no time to evaluate a migration (unfortunately I could not justify a mandate). Are there any guides out there for users of proprietary Reference Manager to migrate to an open source reference manager? I’m interested to know, and I’ll keep that one on the back burner until the next opportunity to convince the customer to give it a try.

It seems to me that Open Source works best when users and developers are equally IT literate. When there is a too strong asymmetry between developers and users, the users tend to prefer the proprietary model in exchange for perceived support. It’s like with financial consulting: individuals will be happy to pay exorbitant commissions to their broker but will not pay a penny for the buy or sell advice, even if trading is a commodity and the real value added lies in the advice. Pay your Open Source developer and you will see dedicated, passionate support.

7 Responses

  1. i personally swear to BibTeX, which has a simple text-file as a database, which makes for very easy backup. I suppose you stumbled over JabRef, which actually is supposed to play nicely with Word using Bibtex4Word, but might be too much for migration.I have never actually used Bibtex4Word, because all my documents that require only the slightest bit of Bibliography are made in LaTeX, and thus I simply use Jabref…

    Did you take a look at Zotero and Mendeley? Zotero might not be the right thing here, since you’ve mentioned that “they barely tried Firefox”, but Mendeley comes with a rather nice Desktop Software.

  2. I have on various occasions looked into solutions here and basically came up empty handed. Your best bet is apparently a bunch of half supported hacks, macros and what not, around (usually) the bib tex format. Storing the references is not the problem. Using them from anything else but Latex is.

    OSS seems to have the storage part of the problem well covered with multiple, redundant, and usually slightly over engineered solutions. Doing such basic things as actually referencing something from OOo and then generating a list of references at the desired point in the text is more difficult. Doing this in the desired format (required by e.g. IEEE) is near impossible.

    OOo has had a bibliography manager that has been ‘under development’ since before the 1.0 release when it was actually relevant for e.g. my Ph. D., which I eventually completed in 2003 (using Adobe Framemaker cross references to keep my hundreds of refs consistent).

    I know people who put up with latex just because of bibtex. I have on various occasions used it but it generally just annoys the hell out of me that I’m chasing compile errors on a bloody piece of text.

  3. Back in university days I successfully used LyX + Pybliographer. Even in 1999-2002 it was a pretty transparent solution. If seems that newer versions of Pybliographer even support OpenOffice.org.

    From what I see, RM exports to XML and bibutils has a xml2bib tool to create BibTeX files that Pybliographer obviously supports. One would have to try that, of course :)

  4. 1. They run the risk of their data being locked in a proprietary format at some point in the future, but right now their tools work most of the time. If they migrate to a new toolset they may find that it doesn’t work at all, and they will have to waste even more time migrating back. If you think a better open source solution exists, the burden of proof is on you to demonstrate that it is better.

    2. I’ve struggled with the reference management problem myself and found that no open source solution currently exists because to open source developers, word processors are a niche market! This is why OO runs slower natively than Office 97 runs on top of Wine on the same machine. And this is why it’s easier to find documentation for installing World of Warcraft than for installing Microsoft Office. And what’s worse, reference management software that integrates seamlessly with word processors is a tiny niche of a niche market. And so, the halfhearted implementation of reference management in OO.

    3. LaTex/BibTex is not practical if your co-authors at other departments and universities are using Word/Endnote. Again, from personal experience. Again, this is not an edge case, is true for many if not most academic users.

    4. In agreement with jillesvangurp, it’s not the database end that’s a problem. The problem is being able to insert citations from the database into an MS Word document (see #3) AND automatically change the format of all the citations and bibliography entries in the document (and they often number into the hundreds).

    5. Linux advocates should just be honest and once in a while admit that there isn’t always a viable open source alternative instead of, in effect saying “my software doesn’t solve problem A, but it’s great at problem B– so why don’t you stop working on problem A and work on problem B instead”.

    As for my own ‘solution’, unfortunately, I’m stuck with VirtualBox, Microsoft Office, and ReferenceManager (same company as Endnote and similar features). Today I downgraded Wine to 1.1.16 (that’s the official workaround to certain installers failing… you just can’t make stuff like this up) and gave another try to installing Office 2000 and Reference Manager or Endnote on a clean .wine directory. Getting better… at least now I can run either Word or RefMan. Just not a the same time: whichever is launched second crashes with a “page fault on read access”. D’oh!! Back to VirtualBox.

    In short, this is a major barrier to academic users (outside CS departments where presumably they all us LaTex) adopting Linux. Even Linux-literate ones like myself.

  5. @F1r3br4nd: thanks for the interesting comments. I’d like to point out that I am not advocating Linux for this case. The operating system is not part of the problem here. The problem is two applications that don’t play well. Since the upgrade their tools don’t work most of the time, and prior to my registry hack solution the university’s own IT department’s only solution was restaging the machines.

    You seem to be making a huge effort to run/adopt Linux. I hope you’re enjoying it or that you otherwise find utility in it. I’m pragmatic. I use what works best for me, whether it is Free or proprietary. All things being equal I do have a preference for Free. The only reason for me to run Windows in VirtualBox is to put an iron-clad layer of firewall around it. The simplest solution I know to run both Linux and Windows side by side is two boxes and a KVM.

  6. Personally I think LaTeX + BibTeX is the easiest way to go, but I understand it’s not for everyone. For integration with OpenOffice.org, I think Bibus (http://bibus-biblio.sourceforge.net/wiki/index.php/Main_Page) is your best bet.

  7. Hello, you might be interested in our tool Docear4Word which is an alternative to bibtex4word. It’s based on the Citation Style Language and offers a comfortable GUI. Although Docear4Word was primarily intended for Docear users, it works with (almost?) any BibTeX file.
    http://www.docear.org/software/add-ons/docear4word/overview/

    And If you are looking for a tool to manage your BibTeX file i would recommend Docear http://www.docear.org/2013/10/17/docear-1-0-stable-a-new-video-new-manual-new-homepage-new-details-page/ :-)

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