Papers in your pocket

Papers is a superb PDF management application for academics. It is very well designed, has great functionality and is beautiful. So I was very excited when Mekentosj the software developers announced that they were making a version for iPhones and iPod Touch.

I signed up as a beta tester for the ipod touch app, so I've been playing with it for about 3 weeks off and on. It was released into the wild a few days ago so you can buy it now for £5.99 ($9.99) from the iTunes appstore. I really recommend this app, I deal with a lot of PDFs in my research and I wouldn't be without this. Definitely worth the money.
I guess you have to have a desktop version of Papers to get the most out of it, but I don't see why if you're not a user you can't just import a collection from the web to your device.

I synchronized with my desktop collection of PDFs and transferred 1000 PDFs to my iTouch. It took a little while, as you would imagine, but was much faster than I thought (minutes not hours). Subsequent syncs are fast as only changes are being transferred.

The PDFs are available by browsing the entire library or in a series of subject folders that I had previously set up. There are listings by author and journal too.

There is an interface to search the web for new articles too. The search options are for the major science journal repositories like JSTOR, Web of Science, Google Scholar and PubMed. It seems to work well, and allows you to import either the reference or the PDF. It displays the journal web page where appropriate, BMC Evolutionary Biology in the screenshot below, and PDF import is straightforward.
PDFs can of course be viewed and browsed in both portrait and landscape orientations. References can be emailed, flagged and notes attached.

This is an amazing productivity tool in a well thought out and well designed interface. I carry all my PDFs with me, and can catch up on reading on the train or wherever. Its also useful in many other situations to be able to instantly check something in a paper (Journal club? Seminar? Coffee room discussion?).

Zotero under fire

Zotero the excellent, free, open-source reference manager is under fire from its closed source competition via a law suit. Thomson Reuters the makers of the unstable and expensive market-leading Endnote software have sued George Mason University, the developers of Zotero, for "violating its license agreement and destroying the EndNote customer base" (Courthouse News Service). The complaint comes primarily from the fact that the latest version can import Endnote styles. I picked up on this from Neil Saunders' blog post who puts it really well

"Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free. There are free-thinking, forward-looking organisations like GMU who see this potential and act upon it. There are also organisations who see only threats to their corporate interests. Publishing corporations no longer control the flow of information to consumers and some of them seem to be struggling to accept this, adapt and move on."

Our support should definitely go to George Mason University who have moved the world forward and improved it with not just a piece of software but a great implementation of the open-source idea. This is software driven forward by users, in this case initially at the GMU's Center for History and New media. Comically there is also a claim that "GMU reverse engineered Reuters' EndNote software to create Zotero". I don't see any signs of that, thankfully they are not very similar in any meaningful respect, Zotero is generally much better. Zotero works nicely from within a web browser, Endnote works when it feels like it.

Zotero is not alone however. There are a growing number of free (though often not open source) web based reference management systems. Maybe Thomson Reuters are just trying to mark out some territory and delay the inevitable a bit longer. Ultimately they are going to fail, I just hope their lawyers don't hurt Zotero too much on their way down.

Using Endnote bibliography styles in Zotero

I just downloaded and tried installing an Endnote style. It worked beautifully. Although how to do it seems obvious to me now, it didn't 15 minutes ago, so here is what I did.

1. Go to Endnote styles page and download the styles you want.
2. Open Zotero and open the preferences pane, choose Styles from the icons at the top
3. Click the + button at the bottom right corner
4. A window appears allowing you to select and import the style from wherever you just saved it

It should then appear in your style list. I just did this for BMC Evolutionary Biology which you can see in the window screenshot given here. I haven't yet investigated whether you can batch import files.

Zotero 1.5 Sync preview

Zotero 1.5 Sync preview is an update to the mostly excellent Zotero reference collection and management software. The big change here is that your references can now be synchronised across machines via the Zotero server. I haven't experimented very much with it since the launch yesterday but after a quick look it seems excellent, a very helpful addition. Another big change that was mentioned is the ability to use more than 3000 Endnote bibliographic styles to format your citations. I couldn't quite see how to implement this, but I only really played with Zotero1.5 for about 10 minutes last night so it might be in there. It requires Firefox3. Now if they could only get Microsoft to fix MS Word 2008 to accomodate bibliography tool bars again we would be there. I saw a blog recently (forgotten where) with someone saying that an institutional licence for RefWorks is around $10k. Zotero is free, and does all the same things, often much better, than RefWorks. It is also a community driven open-source project and needs supporting for that reason alone.

Zotero- have I upgraded too fast?

I might have spoken too soon about Zotero the bibliography tool. Although it looks great in Firefox3 when I actually came to use it today after a while of only thinking about writing stuff I discovered that I had broken it. I upgraded to Office 2008 (OS X) a couple of months ago and the Zotero toolbar only works with the previous version of Word. Also in the past when I have been using ISI Web of Science a beautiful little import button has appeared in the title bar when viewing records and just clicking it imported the reference in to Zotero. Now its gone. WoS has gone through a website update this year and maybe that killed it. So I exported all my references from WoS (in several formats) but couldn't get them in to Zotero. I could see how to get references from other bibliographic tools but WoS no way. I'm sure this used to work for me. The excellent forums didn't help me much on this occasion.

I have used Endnote since my PhD, but it has always been very buggy and unreliable on Macs (unlike PCs I believe). I got to a stage a few years ago where it was almost unusable, and I saw no signs of them updating the Mac version. I bought a copy of Bookends, which was great, but decided not to pay to upgrade to the new version 10 because I saw Zotero as the way to go. I still do, but wish it just moved a bit faster. I may have to spend the money on Bookends though as I can't live without a working bibliography tool. Sad, I see so many really good aspects to Zotero, but maybe I'll have to abandon it until the next major upgrade.