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?).

Turn it off and on again

I said below that Papers (the PDF management tool) may or may not be playing nicely with dropbox synchronisation. I investigated some more and discovered 2 things. Firstly dropbox had stopped syncing, I don't know why, so I restarted it. It lept into action and updated my Papers folder and others from changes I had made last night at home (and had clearly made it onto the server). Secondly I noticed that it had partially mangled my open Papers database, but only for the records that had changed. So for 3 or 4 records I had the info in my local Papers copy (work) but had updated the records at home. It now said that these PDFs were missing. I restarted Papers and now everything was perfect, all PDFs were found, all modifications for records (whichever machine I had made them on) were sensibly amalgamated. Obviously this isn't an ideal situation but at least the tried and tested "turn it off and on again" is a very simple solution to occasional problems.

Dropbox in action

I've been running dropbox on my home laptop and work desktop for a few days now. It seems to be working amazingly well. Very user friendly, very quick. I have moved my data folder for Things (a GTD application) to the dropbox folder and after pointing the application to where its data had moved to it has worked flawlessly. My home and work machines are perfectly in sync. Now there are many other sync options but this one has the advantage of not having to remember to do anything, ever. The application at home and work are always in sync. I do not have to remember to press "sync" or close an application or anything. Remembering to sync before going home has be the cause of the failure at all previous sync strategies using a variety of sync software. Dropbox syncs continuously though in realtime.

I have also synchronised my Journler application. It has worked flawlessly again, even though I have the application open on 2 machines simultaneously (although I am only modifying one at a time obviously).

Papers has not been so smooth. I still need to investigate whether it is syncing properly or whether I am just imagining that some things are not updated. It could be that the application doesn't write some data until it is quit, that would certainly cause problems I guess. More experimentation required.

I have also moved my folder of perl scripts to the dropbox folder. Not only does this sync between home and work but includes a versioning protocol. So if I modify a file I can go back and examine previous versions of that file and revert to one if I have messed things up. I know that svn etc do something similar but this has been idiot proof and has not required all the messing around to install that subversion seems to take.

PDF manipulation

Some journal publishers (e.g. Science) put a really ugly and uninformative cover page on downloaded PDFs. I have been looking at writing a script to either delete the first page of a PDF or to shuffle the first page to the end. I particularly wanted to do this because I use the excellent application Papers to manage my PDF collection. This gives a preview of the PDF by showing the first page- fine unless that is the cover sheet. There are a couple of command line options to manipulate PDFs including pdftk. I was thinking to turn the script into a droppable application and then I could keep it on my desktop and just drop PDFs onto it to convert.

Now just this morning I have realised that this is really easy to do in Preview, Apple's integrated PDF viewer. Just view the thumbnails of the pages and drag the first page to the last. Or select it and delete. I guess it would be good to have a script to batch process lots of PDFs, but this is very straightforward indeed.

I can't believe I didn't realise this before. This is especially useful since Papers has an "open in Preview" command.