Category: Research

Papers 3 for iOS is now free. Good.

I recently wrote about how Papers 3 for Mac has been getting better and that now that they had ironed out many of the bugs, I was once again back using it. So far I haven’t been disappointed.

Some more good news to come out of the Papers 3 manufactory is that their iOS version is now offered for free. While it has dropbox syncing capability, I would stay away from that system and stick to the WIFI sync system if you want to keep your iPad/iPhone and mac based Papers 3 libraries in sync.

Why naming your PDFs consistently matters

I write on my MacBook Air and that is where my main Papers library resides. Each time I import a PDF into Papers, I get Papers to automatically rename the imported file from whatever it was to the following: Author Year Title . Since each PDF gets named the same way, this means that within my Mac, I can do a spotlight search on any of these elements and it is likely that I will be able to find the PDF I am looking for. Although I have many PDFs sitting in my Mac, I can usually remember enough of the detail to be able to quickly find it if I want. Having a consistent naming structure means that I have to spend less time worrying about how to find the original PDFs if I need to.

Syncing my Papers library with dropbox screws with this system. Dropbox needs to create a unique name for each PDF to keep everything straight in its database. Grrr.

The WIFI sync system, however, doesn’t rename your papers as can happen when you sync with Dropbox. This means my PDFs remain neatly filed away on my Mac. This makes me happy.

What’s Papers 3 on iOS like? I can’t wait to find out…

I haven’t used the new iOS version of Papers 3 yet. I have one of the first generation iPads and it is now so old and slow that it is basically unusable. I do hope to become more familiar the iOS version of Papers 3 in late November, however, as I intend to buy one of the new iPad Pro devices. Swoon.

The new iPad Pro will, I think, be awesome for my reading and writing workflows. I’m particularly looking forward to having a screen which is almost the same size as my MacBook Air and the ability to ‘split-screen’. Reading a paper on one side of the screen while having a browser open at the same time makes sense to me. I can search for related papers through my institutional library, check facts with Google or maybe check out the author’s online profile(s). Similarly, reading on one side of the screen while taking notes in, say Byword, on the other feels like it will be a great way to continue to do work when I’m out and about.

If you’ve got a perfectly good iPad and you are using Papers 3 for Mac already, now would be the time to try out their iOS version. At the price of free you’ve got nothing to lose, right?

If you do download it and try it out, I’d love to hear your reaction to it. Feel free to comment below, or tweet me @jasondowns.

Papers 3 and PDF Pen – a match made in Heaven (a workflow)


The problem: PDFs as scanned images (the text can’t be ‘selected’)
The workflow: Extracting PDFs from Papers 3 for mac and OCRing them with PDF Pen and replacing the original PDF with the new OCR version in the right spot
The software: Papers 3 for mac (reference management software) and PDF Pen for mac (PDF manipulation)

The Problem

Managing PDFs is the bane of my existence – well at least on the ‘academic’ side. Fortunately there have been some recent improvements made by the developers of my favourite reference manager Papers 3 for Mac that makes things a bit easier. Finally.

For anyone who has been using Papers for any length of time, you will be aware that Papers 2 was awesome… and then they released Papers 3. We don’t talk about the early period of this release except in hushed tones. I think everyone will agree it is best that it was forgotten. However, with the most recent update (v 3.3.2), Papers seems to be back on track again. Many of the features that were so dearly loved in versions 2.x are back and they seem to have sorted out local wifi sync which means that I can sync my library with an iPad without having to use a third party service like Dropbox (which would do weird things to my file directory/naming conventions).

Like most PDF/reference managers Papers allows me to ‘mark up’ the PDF being read – including extracting quotes, highlighting, underlining etc. This works because most PDFs downloaded directly from the publisher have been OCR’d first. However, if I get a PDF from my University Library Document Delivery service, it usually arrives as an image file. This means no OCR. It also means no clicky, selecty, highlighty, extracty goodness.

Enter PDF Pen by the good folk at Smile Software.

PDF Pen is a powerful piece of software that allows me to alter PDFs in many different ways, but the one I rely upon the most is the ability to OCR a scanned PDF.

OCR stands for Optical Character Recognition. What this means is that the software will look at an image file (in this case a scanned PDF) and if it recognises words in the image, it can convert those images of the words to actual words that the computer can read[Footnote 1].

The Workflow

How to magically OCR a PDF in Papers 3
In the past it has been a nightmare trying to find the actual image of the PDF file within the (hidden) library of Papers 3, extracting it, opening PDF Pen, OCRing the document, saving it somewhere and then replacing the original image file in Papers 3 with the new OCR version. Papers 3 would see the ‘new’ version of the PDF and add it as a supplementary paper, rather than replacing it as the primary paper. Now, with the latest release of Papers 3, the process is much easier[Footnote 2]:

  1. Import scanned image of PDF into Papers 3
  2. Make sure all the metadata is correct using the inspector
  3. Save as a new record in my Papers 3 library
  4. In the inspector panel within Papers 3 right click on the PDF file (see screenshot below)
  5. Choose the option to “open with PDF Pen”
  6. PDF Pen will recognise the image of the PDF as a scanned image and will offer to OCR it for me. Click yes.
  7. PDF Pen does its OCR magic and when completed, overwrites the original PDF image file in Papers 3 with the new OCR version saving it in the same location as the previous image file.
Right click on the PDF image in the inspector panel and then select "Open with PDF Pen"

[CLICK TO ENLARGE] Right click on the PDF image in the inspector panel and then select “Open with PDF Pen”

It works like magic and the PDF is now searchable; sections of text can be highlighted, direct quotes can be extracted etc. all without the messy business of trying to find the original file and making sure that the delicate file structure that I’ve set up is not screwed up.

The fact that the most recent release of Papers 3 now allows spotlight to index the text of the PDFs within its library, it means that I can search for text within any of my PDFs in Papers 3 right from the desktop.


  1. It doesn’t actually covert the text itself, but rather places another layer on top of the document which mimics the underlying text. This makes the text readable by a machine/software. Crucially, it also means that the PDF now becomes searchable.  ↩
  2. If you already have the image of the PDF within your Papers 3 database, you can ignore steps 1 to 3  ↩

Universities as Living ‘Laboratories’

Between March 11th and 13th I’ll be at the National Convention Centre in Canberra, Australia presenting our research on living laboratories. This is part of the Universities Australia Higher Education Conference. This research looks at what it takes for Universities to operate in partnership with industry and develop ‘living laboratories’ where students, academics and  industry can come together to solve complex problems. We’ve managed to do it in my strategic management course which has over 300 students per semester – getting it to work at that scale is tough. My presentation will explain what to do and what to avoid.

I’ve only been to Canberra once before and I really like the place. I can see why @thesiswhisperer moved there to work at ANU.

While I’m there I’m going to take the opportunity to further explore the maps collection at the National Library of Australia and continue on with my other stream of research – mapping. I’m interested in the activity of mapping as being a representative discourse. Specifically, I’m interested in how mapping and the practice of strategy can intersect.

If you are in Canberra at that time, come along to the Poster Hall and say hi. If you are interested in maps, maybe we can go and check out the @nlagovau collection together and nerd out (just a little bit). I’d love to hear about your research and I’ll even buy you a coffee – especially if you know where to find the best coffee in Canberra.