I’m a Mac user, and over the last few years, I’ve wanted to move away from using proprietary software wherever possible. This basically means exchanging MS Word/Excel for OpenOffice, switching my simulation and analysis software Matlab for R, my time wasting literature searching and blogging activities from Safari to Firefox and my reference software Endnote for some freeware alternative.
Unfortunately, Endnote hasn’t had good support for OpenOffice on Mac to date, so I’ve been searching for alternatives that are as flexible across environments and operating system versions as possible, to allow me to make the switch as seamlessly as possible. I have different versions of Mac OSX’s on my laptop and desktop machines, with all sorts of jumbles of software versions and licences meaning I’m a tough customer when it comes to compatibility issues.
So, is Zotero the answer to my long suffering frustrations? The best way to describe it comes from their own website:
Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources.
Martin Fenner has written a couple of posts about reference manager software options here and here, and interviewed Trevor Owens from Zotero so I’d like to take this opportunity to state that I’ve spent the last couple of days road testing Zotero as follows:
- on different machines (PPC and Intel Macs),
- running different versions of the operating system (OSX.4, OSX.5),
- different versions of Zotero (Zotero v.1 on the PPC OSX.4, Zotero v.2 on the Intel OSX.5)
- different word processors (OpenOffice v.2.4, Word 2004 & 2008)
Good boy! Zotero sits nicely in the bottom of your foxy web browser.
and so far, I’m reasonably happy with it’s within species performance. Installing the required plugin for Citation capability in OpenOffice was a bit sticky, but it seems to work nicely now.
Importing my reference library from Endnote was straightforward1. Once imported, I basically want to use my reference manager to stick in article citations when I’m writing a manuscript and generate a bibliography at the end of the paper.
Insertion of the citations is done easily in Zotero, and produces a lovely bibliography at the end. There are only a few output styles included in the basic Zotero download, but others are easily available, if a little tedious to install – they seem to need to be installed individually.
Endnote begone! I will switch my CWYW allegiances to Zotero!
Zotero also easily finds and incorporates citation information from webpages into your own database, e.g., downloading citation information from a doi accessed webpage, simply by clicking an icon in the address bar.
The major problem I’ve found so far is backwards compatibility. It doesn’t manage to switch the same document between different versions of Word (2004 vs. 2008), due to the different versions of Zotero required for older and newer Word versions (v.1 for 2004; v.2 for 2008). Documents are viewable, but citations are not editable.
Moving from OpenOffice (2.4 on the PPC) to Word 2004/8 wasn’t possible. This seems to be a problem with OpenOffice’s ability to save the documents in a sufficiently recent Word version (the most recent offered was Word ‘97/2000/XP), and Word’s inability to read and convert *.odt documents.
One further potential downside for avid Mac users is that Zotero only has limited compatibility with Pages 2 and for all users, limited compatibility with Google docs. Drag and drop bibliography lists are allowed, but I haven’t found out how to Cite while you Write in these environments yet. These are projects I hope Zotero are already tackling, but they’re doing a reasonably good job so far.
There are more features I haven’t even begun to explore yet, such as storing your reference database online for easy switching between computers and sharing info with collaborators. This last option will be useful to me as my tame PhD. student has just moved to Canada, and we still have joint projects to work on.
In conclusion, I like Zotero. It’s intuitive, does exactly what I want it to do within my manuscripts, works well with OpenOffice, but needs a bit of work for moving between systems, which will be important for the collaborative claims made with online functions. But most of all, it’s good cos it’s FREE!
1 Export as a Bibtex library (Endnote 9) or RIS format (Endnote X2).
2 Even though Pages is proprietary software, I have a copy installed, but I try to avoid using it where possible. Google docs functionality would be much more appreciated.
Uh, what exactly is your beef with proprietary software?
Put simply, for the hard of understanding, £$€¥.
Almost all of my work is computer based (unless I’m feeling brave, when I might use a pencil and paper), so I notice when (& why) things don’t go smoothly, then get to thinking “why does it cost me (or the grant money) so much money in licence fees when it’s full of bugs anyway”?
I’m moving to a new position in a new country soon, where money for scientific consumables is not necessarily as freely available as in other countries. This means that software licences may not be as up to date as I’m used to, or even as extant as I’m used to. In this case, freeware can offer more up to date and superior solutions, at no extra cost.
Further, if I can reduce costs to myself and my institute, there will be more money for other essential things, like travel, or publication fees for OA journals. Yay for free things for people!
Safari, if you’ve already bought MacOS, is free.
So your logic isn’t.
PS Actually, Safari is free on Windows, too.
Pages isn’t so expensive – and you get it as part of iWork which also has a spreadsheet app (Numbers) and the wonderful Keynote. And, Pages is now compatible with Endnote which, from your description, still seems much more polished than Zotero.
I know this is a changing landscape but for me the reality is that most of my co-authors use Word and Endnote so that dictates my usage.
Mike I’m glad that your experience with Zotero so far has been positive. I often hear (and use) the argument that all co-authors use Endnote as the main reason to use it. Which is understandable, but doesn’t say anything about the quality of the software.
Safari may be free, and Pages relatively inexpensive, but the source code for either is not freely available. This means users are restricted to the upgrades that the software owners want to release, which will be based on usability and commercial reasons. For packages where software is open source, users can constantly contribute bug fixes, new features, “upgrades”…
I’m not really sure how much more polished Endnote is than Zotero – the post was mostly about my first experience with Zotero, so I didn’t go into pros and cons of other reference software. Endnote may work well with different versions of Word and within releases of Pages, but because of between release compatibility issues with iLife ‘08 and ’09, Endnote isn’t a good solution for people using different versions of Pages. Endnote doesn’t have all the same features as Zotero either.
Incidentally, while Keynote ‘09 is pretty sweet, it also has back compatibility problems. I always end up converting any presentations I make from the package used to create them, to pdf. This is the best solution I’ve found to avoid any cross-version or -platform issues.
Which, for the hard of understanding, is why I asked what your beef was. Because, you see, Safari might be closed source, but the underlying engine, Webkit (a nifty browser in its own right), ain’t.
Richard, Safari was a poor example. Not so much of a problem with the logic though. Perhaps you should get to your point a bit faster in the future – even if it is a trivial one.
Martin & Stephen, I think there are serious problems with the “everyone else uses it, so I might as well”. This will ultimately lead to a reduction in choice for users. In my experience, IT units are set up to make the lives of IT staff easier rather than the researchers. Of course, I understand that setting up a secure system that students can use is a major part of their job, but doing research efficiently should also be a driving force behind decisions.
In practical terms, different Universities will have different software deals, sometimes making it difficult to work on the same MS with collaborators. I couldn’t even get my boss to use Endnote, and he sat in the office next door to me.
My point was that Safari is free, and that the core is open-source. Perhaps you should do your research better.
I think there are serious problems with the “everyone else uses it, so I might as well”. This will ultimately lead to a reduction in choice for users
Nah! “Everyone” doesn’t mean nothing. Innovation doesn’t care. New things/software etc comes along all the time because someone has a good idea and moves the curve. Everyone used DOS…for a while. Everyone used IE…for a while.
Peole will use the easyest and most accessable. If “everyone” else is using it you have a built in usergroup to rely om
Ian, I disagree and thing that the “everyone” factor should not be underestimated. Not only is it much easier to ask for advice if the people around you use the same tools, but it is also easier to collaborate. So the new tool has to be much better (or cheaper) or people will not switch. Papers is significantly better than Endnote to handle the fulltext PDF files of scientific papers, so I switched. I like that Zotero is free and open source, but more importantly it has to be much better than Endnote for putting references (exported from Papers) into my manuscript, or I will not switch. If the coauthors of my next paper don’t own Endnote (which is expensive), I would use a different tool, e.g. Zotero. But this might also be RefWorks (our institution has a site license), but not Mendeley (no Word or OpenOffice plugin for Mac users yet).
Big on my wish list is a common word procesor plugin architecture, so that everybody can use his preferred reference manager.
Ian, I guess I was getting at “everyone” in academic institutes, paricularly universities that teach and research. I agree with you that innovation will move along because some businesses and personal users will always want or need state of the art software, but (again, in my experience) academia tends to lag behind other sectors in IT terms1.
I have a copy of Papers, but haven’t found the motivation to really test it. Again, it doesn’t quite fit in with my ‘freely distributed’ profile. When something is free, and importantly, easy to use, I can suggest it to collaborators independently of their institutes’ IT resource/support availability.
More generally, public money doesn’t need to be spent on software licences. There was some muttering recently about the UK civil service shifting to open source software where it delivers the “best value for money”. I personally would rather my tax money was spent on employing suitably qualified individuals to run these systems, than lining the already well lined pockets of large software corporations.
1 Actually, I also worked in the Financial sector for a while, and their IT capabilities weren’t too hot either. I for one shall not invest money in a certain shabby, national UK financial institution. After all, as Groucho Marx didn’t quite say, “Good grief, they employed me, so I certainly wouldn’t trust them with my cash”.
Just to give a little support to Mike here, OOo is a good application for academic writing (certainly better than Pages in my view), and is not only free, but cross-platform. The same is true of Zotero. The new groups functionality in Zotero makes collaboration quite convenient, and goes way beyond alternatives like Endnote.
So the combination is a really good choice, is free of cost, and offers you the flexibility to easily move back and forth between different operating systems as you need/like.
I can understand the need to move away from proprietary software (which is why I use Linux, in addition to OS X and Windows). However, there are some situations where absolute compatibility becomes vital, and if your collaborator or client is using a certain proprietary package, then your best bet to minimize problems is to do the same.
I use NeoOffice for most basic “office”-type documents and it works really well. However, the occasional Word document that is 300+ pages long, with lots of embedded objects, can bring it to its knees.
One thing you haven’t mentioned is support. Although one can rail on and on about certain commercial vendors and their
shittyshabbynonexistantdoubtful-at-best support, the main reason I prefer to stay away from free software is that I, like 99.9% of everybody, am no good at fixing it. Source code and so forth is all very well if you’re a programmer, but if you’re not, it’s of no use whatsoever.So, I will grumpily stick with MS Office and continue to complain about it in the time-honoured tradition. Although the idea of running Linux+OpenOffice, etc. appeals to me (and I said that somewhere else too, darned if I can remember where though), I’d rather pay the $ and have something with documentation, upgrades and support.
Support is an issue, but a complex one.
The best support is an application that doesn’t need it (e.g. is free of bugs, and utterly intuitive). Absent that, there are many ways support happens. In the Zotero world, beyond the core developers, there’s a large community that is happy to help. So it’s a common occurrence, for example, that someone has a problem with a style, and a volunteer fixes it in a matter of hours. This sometimes happens with the code as well.
Compare this to some commercial developers (like the ones behind Endnote) that only issue bug fixes as paid upgrades, and have failed to fix long-standing bugs (say Word’s master documents functionality, or Endnote’s RIS export).
So while buying commercial applications may give one a sense of security, I personally think it’s illusory. At the very least, one should probably look at the specific applications and features in question, rather than to assume generic conditions.
Bruce, thanks for the support! I don’t have any experience of using Endnote Web – perhaps this makes collaboration around the world more straightforward? However, this is restricted by the next point…
Ken,
This only works if your institute/organization has access to the same software as that of your collaborator. This just ain’t always the case. e.g., if your organisation doesn’t have a licence for Endnote (Web). Using freeware/non-proprietary software means that the same software is potentially available to everyone!1
And to echo Bruce’s 2nd point, in answer to Richard’s doubts about support, most freeware/open source packages have a stable release available, which has as few bugs as possible. Certainly should be comparable with proprietary software in terms of stability. Therefore, no knowledge of coding is required to use pretty solid versions of OpenOffice or Zotero.
For the more adventurous, you can use/test alpha and beta versions which are more cutting edge, but less stable, with users offering feedback where possible. These are not recommended for using with any important documents, as crashing may be fatal for them.
1 Assuming your IT overlords haven’t disabled your administrator rights – blocking you from installing programs – as happens to many PC based researchers at Helsinki University.