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It started with a Bamboo...

20/1/2013

2 Comments

 
I have a sick feeling in the pit of my stomach, and the muscles of my right shoulder are aching.
The cause of my malady? Trying to find a goddamn note-taking system for my PhD that works.

It should be simple. I should read the PDF papers I have, take some notes, and write relevant information into the papers I'm currently drafting. But I've spiralled into a vortex of note-taking software and hardware.
Picture
It all started when I decided to borrow a Wacom Bamboo tablet. I wanted to devise a paperless note-taking system that still allowed me to hand-write notes, and it seemed that the Bamboo tablet was the answer. Hand writing notes versus typing them out has always been my preferred modus operandi. The Bamboo would allow me to write digitally on PDFs, and ta-da! Perfection. Only problem was, I had no idea what software to use.

ALL the PDF annotation software
I searched extensively for a program that would let me handwrite over a PDF using the tablet, that works on Mac OSX and Windows 8, that is also free. Not as easy as I'd hoped! As it turns out, the best programs aren't free (PDF Annotator, Inkbook) or don't run on Mac (AutoInk plug-in for Adobe Acrobat), and the free ones don't easily allow annotation (PDFPen forces you to re-select the pen tool every time you write a new character), or don't allow for smooth writing (Skim, Adobe Acrobat).

It might sound fussy, but when the alternative is cheap paper and my legible handwriting, I want the best I can get. The Bamboo tablet did come bundled with some software that allows you to annotate a virtual note-book (Bamboo Paper - but the handwriting isn't very smooth), or write on screen and it translates it directly into text (Bamboo Scribe), to be pasted in any application. And in fact, the Mac OS allows you to do this too (Ink). But this is just a scratch-pad, and I really wish they'd let you save what you've handwritten, because Bamboo Scribe was the smoothest/neatest by far!
Picture
I really enjoyed looking through approximately one thousand search results that didn't quite lead to
the software I needed.
Too many programs, not enough time?
This leads to a second problem: integration of different methods/software. At the moment, I use Mendeley to read and annotate journal papers, and as my citation software when writing up my own results. But if I'm annotating PDFs in Mendeley, do I really need another piece of annotation software just to handwrite on them? And I'm currently using Scrivener to draft up my first papers, which has a 'research' area that allows you to pin PDFs, write notes, add pictures... again repeating what Mendeley can do to some degree. And I've heard of other people using Evernote to write up notes and sync information across multiple devices, which would come in handy when jotting down notes on my phone. But again, double-handling is the issue. Or is it...
Bamboo + Evernote
As I though more deeply about this problem, I realised that although Mendeley allows for detailed analysis and note-taking on individual PDF papers, there is no space write about broad scale topics which span a number of papers. You can tag numerous papers with the same subject, such as 'taphonomy' or 'burial', but there is no way to combine all the information from different papers in one document. So why not just use Scrivener to do this? Well, the page layout isn't as conducive to note-taking in this way, but rather drafting and word-processing. Plus, it isn't available on different platforms (WP8 specifically) or online like Evernote is.

During this research, I found out that Evernote (on Windows) allows you to use a Wacom tablet to write directly in the program. Problem solved... or is it? To my dismay, this function is not provided in the Mac version of Evernote, but a work-around using Evernote Skitch to annotate images and import them into Evernote almost works just as well.
The master plan (trial version)
Evernote seems to be the solution to my woes, so I will trial writing up thoughts and ideas that come from reading papers in Mendeley, by creating a .jpg of the Cornell Method template to write onto in Evernote. This way, I can access this information wherever I am, and especially during meetings with my supervisors. I will still use the tagging system in Mendeley, so it will remain my referencing and citation software. But trains of thought and brainstorming will remain in Evernote.

Oh and the pain I spoke about before? That sick feeling that I've wasted a weeks worth of work just trying to figure out the best way to be productive. Add in a sore shoulder for not using a proper ergonomic set-up for the tablet (it was sitting too far to the right when it should have been centered in front of me). I'll keep you up to date and let you know if it was all worth it!

2 Comments
Cassady
17/4/2014 09:00:17 pm

Hi!

I stumbled across your page - going through the same process... Not happy reading unfortunately - mind-boggling that so few (if any?) companies have seen this as a gap in the market, that I'm sure many academics would jump on.

I use Scrivener, with Bookends on my Mac. My DB manager is Devonthink Pro Office, which I love. Even though I played around with Skim - I simply couldn't find anything on the mac that makes annotating easy. Even simple annotations (such as highlighting text), invariably results in far too many button-presses, if heaven forbid, you want to use more than one colour for each, separate 'point' that is worth highlighting on the page...

My workaround involves using DevonthinkToGo, to get the pdf onto my iPad, and into Goodreader. It does a fair job, and at least using the stylus on a tablet, is closer to the 'real-world' scenario of annotating actual, printed pdfs...

But there comes a time, regularly in fact, that I want to annotate a 'fresh' pdf on my Mac - right there and then, when I'm in the moment - and it sucks.

I too started looking at Wacom, and rather disbelievingly realised it doesn't focus on pdf annotations... I cannot get my head around that - surely it would make so much sense to allow for someone to open a pdf on screen, and then use the Wacom etc. as if you were drawing on/over the actual document?

I swear that the above might just see me finishing my dissertation, and then teach myself coding, if only to write my own darn app, that will allow me to do this...

Please shout if you've managed to find something since you posted the above! And hope the shoulder is doing better!

Reply
Caitlin Syme link
23/4/2014 11:09:43 am

Hi Cassady!

Ahh, I've always wondered about using DevonThink... I might try it out now!

I've now resorted to typing notes in Mendeley, and compiling them in a mind mapping program (XMind) to make nice links between topics. If I'm having particular trouble with a paper, I'll print it out. But I'm still looking for good solutions!

I bought a tablet computer and stylus, and tried annotating PDF's that way, but there still aren't many Windows apps that can handle inking well.

I have actually found another solution, but it's very pricey and PDF only: the Sony Mobius, a 13.3 inch e-reader (shipping in May, apparently).

http://www.maximizingprogress.org/2014/04/digital-paper-sonys-a4-featuring-e-ink.html

But I definitely won't pay over $1000 for something which may not be the ideal solution after all! Maybe I could offer to review it in a academic setting...

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    About the author

    Dr Caitlin Syme is a palaeontologist studying the taphonomy (preservation state) of fossil non-avian dinosaurs, crocodiles and fish from the Winton Formation, Queensland, Australia. Think forensic science or CSI for fossils, and you're on the right track!

    Posts on this blog focus mainly on vertebrate palaeontology and taphonomy, as well early career researcher (ERC) productivity tips and insights.


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